2004 R53 (re)Build Thread

Discussion in '1st Generation: 2002–06 R50, R53 & 2004–08 R52' started by trevhead, Feb 20, 2021.

  1. trevhead

    trevhead Active Member

    Apr 15, 2019
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    Hi everyone. I'll be documenting a big job (for me) to both solve a major problem and take care of many aged parts, and hopefully solve a persistent oil leak that has evaded me so far.

    This is a 2004 MCS six-speed. I'm the original owner and it is now my 18-year-old son's daily driver after being my daily for 15 years. It has 152,000 miles and has been well-serviced by two mechanics throughout its life, and by me for the last few years.

    This all started over here where I was troubleshooting codes p0302 for a cylinder 2 misfire, along with p0456 for an EVAP system leak. Thanks to several of you who helped me out over there (MCS02 and Myles2Go, and others!) That thread ended with my mechanic finding the main problem - a burned valve on cylinder two.

    We're now digging into the following:
    • pull the cylinder head
    • cylinder head to machine shop for valve job
    • new timing chain
    • new timing tensioner
    • new chain guides
    • new oil pan gasket
    • new crankshaft position sensor o-ring
    • new oil filter housing gasket
    • new belt tensioner & pulley
    • new supercharger pulley - Cravenspeed 15% reduction
    • new crankshaft pulley - Cravenspeed 2%
    • new idler pulley
    • new crankshaft seal
    • new belt
    • new valve cover gasket
    • new timing cover gasket and seals
    • and of course, new oil and coolant
    I'll document this work with a summary of each day, photos wherever possible, and almost certainly some questions along the way.


    In May of 2020, we did what I thought was a major refresh. Oh how innocent I was... at that time, we:
    • removed the supercharger and replaced its oil
    • replaced the green supercharger-to-block gasket
    • replaced the supercharger-to-charged air plenum gasket
    • replaced the throttle body gasket
    • replaced the valve cover gasket
    • replaced the spark plugs
    • replaced water pump outlet o-rings
    • replaced the belt
    • replaced upper and lower radiator hoses
    • replaced the radiator
    • replaced both oxygen sensors
    • replaced the exhaust manifold & cat (original manifold cracked, which led to this work in the first place)

    Fair warning - I think I work pretty slow! I doubt I'll be posting up huge progress each day, and to make it worse, I'll probably only be getting into this on the weekends unless I get really deep in it and take a day off work. I'm no pro, I'm learning from YouTube, forums like this, and my new Bentley manual and the Haynes manual we've had for a few years. I take my time, bag and label parts and hardware, and stop when I'm tired (or my garage gets too cold - it's awful right now).


    Day 1
    Got a slow start, but set a goal to lay eyes on the crankshaft by the time I was done, and I managed that much. I also got my first look at just how bad the oil leak really is. The horizontal surfaces are covered in oil from the front of the block all the way back past the power steering fan. It's not good. Really hoping the gaskets and seals I replace will solve this.

    Today we accomplished:
    • front-end service mode with the radiator frame supported on 8mm x 100mm bolts
    • removed the power steering fan to get it out of the way
    • drained oil
    • removed lower engine mount; rubber bushing is cracked, new one on order
    • removed the serpentine belt
    • removed AC compressor
    • pulled the crankshaft position sensor, replaced o-ring
    • removed the oil pan
    • removed the intercooler
    Lots of little bits of metal in the oil pan... I'm really not feeling good about that. It's been years since the oil pan was off - the gasket was last replaced at 110,000 miles in 2016. That was done by my mechanic, and they reported a clean pan at that time. So all these little shavings and flecks are from the last 40,000 miles. I change the oil every 5,000 to 6,000 miles with LiquiMoly Molygen. I'm not sure yet what to make of this, but it seems it could be bad news for the state of the engine internals.

    Nasty Engine Mount
    Oil Pan & Gasket
    Crankshaft, wiped down
    Crankshaft
    Look at all that mucky oil on everything
    Clean oil pan interior
    Dirty oil pan exterior (to clean tomorrow)


    Tomorrow's plan is to detach the exhaust manifold (and heat shields) and pull the oil filter housing for its new gasket. Then I'll get the new oil pan gasket and oil pan back in so I can get my jack under the pan to support the engine for removal of the belt tensioner and pulleys. But the cylinder head is my priority - I may get those other steps complete to be ready for the pulleys, but I want to get the cylinder head to the machine shop on Monday, so that's my primary goal for tomorrow. I'll share progress tomorrow night.
     
  2. MCS02

    MCS02 Moderator
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    Excellent thread! Your right metal in the pan is not a good sign. The bottom end of that motor is built like an anvil. I can’t imagine whet is making metal.
     
  3. trevhead

    trevhead Active Member

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    I've ordered a test kit from Blackstone Laboratories. I'll transfer the drained oil into a clean container so I can check it out when the kit arrives, should be one to two weeks according to their site. Meanwhile, I'll carry on... need to fight through the morning-after sore shoulders and back!
     
  4. trevhead

    trevhead Active Member

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    Day 2
    My goal today was to get the cylinder head out. I want to drop it off at the machine shop tomorrow so he can have it all week if necessary (expected lead time about three days, but might depend on if we need to replace any parts with the valves and springs etc). After about 10 hours of hard work, the head is out! Among other things. Today we accomplished:

    • new oil pan gasket and oil pan re-installed
    • pulled the exhaust manifold free from the block
    • removed the oil filter housing and replaced its gasket; re-installed the filter housing
    • removed the DME and the airbox, along with the air intake tubes
    • drained coolant
    • removed the fuel rail
    • removed the valve cover
    • pulled the camshaft pulley and freed the timing chain
    • removed the chain tensioner and chain guides
    • finally removed the cylinder head!

    Not much of a list for 10 hours, is it? It is so much work to get through everything to finally get to the head. And I really took my time with the oil pan and filter housing, I've never done those before. Just finding the damn bolts for the filter housing was probably 45 minutes! ModMini's video on YouTube is my savior. I had that up all day long, play a few seconds, pause it, do the work, go back. I'd switch between that video and the Bentley manual to be sure I was catching everything.

    Oil filter housing, old gasket. It has about 42,000 miles on it. I'm not sure of the lifespan for these, but that seems not so old. But there was oil seeping out at the bolts, so this was at least one source of the constant leaks.

    Rockers. They look awesome. Everything here appears to be in fantastic shape, no grooves or marking on the camshaft or the brackets. The brackets popped right off with my hands very easily, as I believe they are supposed to.

    Found a broken bolt in my throttle body housing. At the top of the photo. I did that last May, apparently. That's the last time the throttle body was out and back in. Dang. I've never had to resolve to broken-off bolt in a housing like this, I don't even know where to start with getting it out. Maybe possible to get pliers on the little bit sticking out to back it out? Haven't tried yet.

    The main event! The valves do not look so good. Although I'm not exactly an expert. Looking at cylinder 2 (this is oriented 1 through 4 from left to right in the photo), I can tell it is burned. Thing is, cylinder 1 looks about the same, 3 isn't much cleaner, and 4 does appear to be cleaner but not great. Although I'd imagine there is going to be a lot of this dark build-up after 152,000 miles regardless of a major problem. At any rate, I can't wait to see this after the machining and valve job.

    The block and cylinders. I have shop towels stuffed into cylinders 1 and 2 to sop up the mess you see in cylinders 3 and 4. There was coolant pooled on top of each cylinder. That had to have come from lifting out the head, right? It would be all chocolate-milky if it was actually mixing up in there, correct? Bigger question: Do the tops of the cylinders look okay or normal? There is a a lot of built-up grime and crust on them, and I don't know if that is to be expected or not. Either way - should I try to get those clean, and if so, what are the preferred methods or materials?

    Two days of work, all organized and waiting to go back in.


    I'm sore and exhausted but pretty satisfied with the first weekend. I doubt I'll get into much if any of it during the week this week, but I'll share updates about the valve job progress if there's anything noteworthy. Other than that, I'll be back next weekend, hopefully with a clean and fresh cylinder head to re-install. But first, I'll be getting into replacing the timing chain, tensioner and guides, and the crankshaft and supercharger pulleys. And tensioner. And idler. Miles to go here.
     
  5. MCS02

    MCS02 Moderator
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    For the broken bolt I would put some penetrating oil on it and let it soak in first. Then if you can get a good grip on it with some vice grips that should do the trick, just get them on good and tight. The other option would be to cut a slit in the broken bolt and use a flat head screwdriver to get it out. If nether of those work you will have to drill it out. I am very surprised you did not have an air leak because of that broken bolt. Perhaps you did causing the motor to run to lean and thats what burned the valve. Oh also put a shop rag in that opening, you don't want anything falling in.

    If you did not drain the block then you still had antifreeze in the head. Not a problem. You may want to take the drain plug out of the oil pan to get any antifreeze out that went down to the pan when you removed the head.

    I think the pistons look ok its hard to tell. from the picture it looks like just carbon build up except where the antifreeze sat on them. If you want you could clean the carbon off the tops. Just be gentle and don't gouge or scrap up the tops of the pistons. Also get the pistons at the top of their stork to wipe them clean. I am picky but I would use a shop vac to get anything that falls down on the rings.
     
  6. trevhead

    trevhead Active Member

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    great advice, thanks - pretty much describes what I planned on doing.

    Got the head back yesterday, it is beeeeyooooteeeeful... shame to put it back in and hide it!

    I had the same thought as you re: the broken bolt on the throttle body, that was a likely cause of this whole situation. I broke that (unknowingly) when I reassembled everything last May. It seems plausible that it's been causing it to run lean ever since. That relatively short amount of time might also explain why the guy that did the valve job said yes, the valve is slightly burned, but really not bad. The bigger valve issue was that they were out of round and he corrected that. Besides that he said everything was in really good shape.

    Back to work on everything tomorrow. Pulleys, timing chain and reinstalling the head, hopefully all done on Sunday and we start it back up by the end of the weekend.


    [​IMG]

    [​IMG]
     
  7. 00Mini

    00Mini Well-Known Member

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    Head looks great. Hope your reassembly goes smoothly.
     
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  8. trevhead

    trevhead Active Member

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    Day 3

    Fairly short day of work today. We took a detour to a junkyard and pulled the front seats out of an '05. Our drivers seat cloth is wrecked, years of wear finally got exponentially worse and it's torn in two big gashes on the seat back side bolster and the stitching is giving out. Now we have two dirty but very cleanable black leatherette seats to swap in that will clean up the look quite a bit. I'll miss the two-tone space gray cloth though tbh.

    Today's work:
    • Removed belt tensioner assembly
    • Removed crankshaft pulley, idler pulley and supercharger pulley
    • Removed timing case cover and cleaned
    • Removed timing chain
    • Installed Cravenspeed 15% reduction supercharger pulley
    Stopped there for today. I need to sort out what I'm doing next, seems I could go a few directions but I think my best move is to get the head back on first thing tomorrow morning so I can get the new timing chain installed easily with the cam sprocket able to go back in place.

    Found something odd tonight, unsure what it is and it seems like I should probably worry about it... can anyone tell what this plastic plunger-like piece is? It has two springs, the obvious one on the outside and smaller one inside, so that end presses like a button:

    IMG_0663.jpg

    I found this by accident. I looked down at the oil filter housing and it was just sitting inside oil filter housing, resting loose on the threaded side of the housing where the filter and cap would be. I put the filter housing back in last weekend after changing the gasket, so somehow this piece ended up in there since then. It appears to be broken - you can just see three prongs inside the large outer spring, it's hard to tell even in person but they appear to have snapped.

    Is this a part of the oil filter assembly, maybe something that the filter presses down into when it's being pressed in? Seems like a speedbump for me to clear.

    Another odd thing discovered: When I removed the timing case cover, there was no bolt where bolt number 1 should be (lower-most right corner of the cover). I've never touched the timing cover, and I can't actually think of a time that a mechanic would have either. Bolt 11 was barely finger-tight... do these back out over time from vibration? I'll get a replacement for bolt 1 tomorrow, they look to be 20mm. I'm actually encouraged that this could have been one of the sources of the constant but minor oil leaks.

    I think my plan tomorrow is to reinstall the head, get the new timing chain and guides and tensioner in, then replace the timing cover, pulleys and belt tensioner. I'll be putting on the Cravenspeed 2% crank pulley. I can not believe how much lighter it is than the stock crank pulley! Pretty excited about that.
     
  9. MCS02

    MCS02 Moderator
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    That belonged in the oil filter housing. Did you say you had low oil pressure at idle? That will cause it. You may consider replacing the oil filter housing with a new one.
     
  10. trevhead

    trevhead Active Member

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    luckily I never have had low oil pressure warnings, I believe this happened during this work for the first time. Amazingly, and ironically about at the exact same time you replied last night, I found out what the part is. It's the drain block valve for the oil filter housing. Used to be you had to replace the entire housing when those broke, but now OutMotoring sells a 3D-printed replacement part for $30. It's on the way. You're correct that it would cause constant low oil pressure warnings if I put it back together without the drain valve.
     
  11. MCS02

    MCS02 Moderator
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    Excellent, I didn't know they had them.
     
  12. trevhead

    trevhead Active Member

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    https://www.outmotoring.com/MINI-Cooper-R50-R52-R53-oil-filter-housing-drain-plunger-spring-repair-kit-rep_12345.html

    I found this by stumbling on to an article at MiniMania about the oil filter housing, I didn't know what I was looking for but I figured I'd start there. Their article showed a picture of the inside of the filter housing and I realized what the part was, and they had it labeled so I knew what to look for after that. Found forum posts from several years ago from a guy who started 3D printing them because people were trying, with mixed results, to replace these with whatever was available at parts stores. They seem to be close but not quite. Then that guy got his 3D printed part into OutMotoring, I went there and sure enough, 30 bucks and I'm set.
     
  13. trevhead

    trevhead Active Member

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    Day 4

    Major progress, but not done yet!

    • Cylinder head back in
    • Exhaust and intake manifold reconnected
    • Camshaft and rocker arms back in
    • Cam sprocket in place and new chain hooked up, aligned and timed
    • New chain guides in
    • New chain tensioner in
    • Timing case cover back on
    Somehow, that's it... the exhaust manifold screwed me so bad today. Embarrassingly, I wrestled with that thing for about two hours. I know that sounds ridiculous. Just could not get it to line up. I still have the engine on the jack and I kept raising and lowering to try and match it up, eventually I did hit the right height to allow to to line up. Until then I just kept doing the dance of getting one bolt in, then the gasket would slip, I'd get that back, but I could never get a second bolt to line up... I don't ever want to do that again. That part of the engine was designed by goblins.

    I tried but failed to drill out the broken throttle body bolt. I've put the throttle body back in with the three good bolts, and I'll get it to my mechanic for that one thing, let them use the right tools to do it. My big drill is too big to get a straight shot at the bolt past that air supply horn, and my small drill isn't powerful enough to get the bit into the bolt. Once up and running that's the first thing I'll do. And I may ask them to do a smoke test and a compression test just to be certain I've buttoned everything up properly anyway.

    I'm taking a day off work tomorrow to hopefully finish this up. I won't have my oil filter housing drain valve by tomorrow, but if I get everything else done I'll probably go ahead and start it up to make sure the timing is correct and to check for leaks. I guess I'll have to expect a low oil pressure warning if I do that. Tomorrow will be the new pulleys going on, new lower engine mount and then putting all the bits and pieces back into place, reconnecting the fuel rail and plugs and vacuum lines, etc. Hoping to turn it over and see what happens at some point tomorrow.
     
  14. trevhead

    trevhead Active Member

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    #14 trevhead, Mar 1, 2021
    Last edited: Mar 1, 2021
    Day 5

    Done and very happy with the results! Long final day today as I cleaned a lot as I went through the final installations and then the long process of buttoning up everything that had been dismantled.

    New pulleys are in, new belt tensioner and new engine mount as well. Everything went back together without drama.

    First drive - lots of grinning and chuckling from my son and I! We’re actually amazed at how different and better the car feels. So much pep and zip there that had been long-lost. The 15% supercharger pulley and the lightweight crank pulley are game changers. Kicking myself for waiting this long... I could have done this 100,000 miles ago!

    The car has a new lease on life.

    Couple of details to sort out next:
    • The oil filter drain valve will be here this week. I filled it today with cheap oil that I’ll drain by the weekend and refill with my preferred LiquiMoly. At that time I’ll get the drain valve in and lose the oil pressure light. Only on at idle and low revs as expected.
    • Speaking of idle - it feels low or rough. Not intermittent or missing, and not hunting. Just rumbly and a touch uneven. No codes for the obvious like a misfire (I cleared out my old codes for misfire and evap leak and they didn’t come back in tonight’s drives, only about 25 miles so far though).
      I put in the cooler-running NGK plugs that the JCW used, because of the reduction pulley... could that cause it? Like an adaptation issue? Actually just thought of that. I didn’t reset the adaptations... would they anyway after the battery was disconnected for 9 days?
    • Or, could it be the low oil pressure at idle from the missing drain valve in the filter housing?
    • I’m going to get it to my mechanic to deal with the broken throttle body bolt, hopefully this week. I want that sorted ASAP. Maybe causing the idle rumbles?
    Thanks many times over for following and replying with encouragement, ideas and your experience. This was a MEGA project for me, by far the biggest car project I’ve ever done. The idle is nagging at me but overall this feels like a big success. The car feels fantastic now. And we love the louder supercharger whine.
     
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  15. 00Mini

    00Mini Well-Known Member

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    I wonder if the lightened crankshaft pulley is causing the rough idle.
     
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  16. MCS02

    MCS02 Moderator
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    Chad at Detroit Tuned told me the adaptives have to be reset. He said it was a myth that unplugging the battery reset them, but that could be part of the problem. I am sure it’s not the plugs those are what I ran in my R53. @00Mini has a good point. Small chance the throttle body is causing the problem. Is may be letting a little unmetered air by the broken bolt.
    Congratulations on getting it back together!
     
  17. trevhead

    trevhead Active Member

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    Those are good ideas... I called Detroit Tuned this morning. He didn't straight-up say that the pulleys require the ECU reset but he thinks it might help. I get where he's coming from on not committing to that as the answer, because who knows, I could have a vacuum leak somewhere in all my re-assembly that's causing the wonky idle as well. But the logic behind clearing the adaptations makes perfect sense to me. The computer is governing the engine based on physically-different criteria than it has to deal with now.

    I'll work on the adaptations today/tonight and report back. Still think the throttle body maybe has something to do with it, but it seems it would have idled like this before if all it took was that one small weakness from the broken bolt. Either way, I'll get that resolved asap.
     
  18. trevhead

    trevhead Active Member

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    Cleared adaptations yesterday and that did stabilize the idle a bit, it’s smoother and improved.

    I now have a code for lean mixture (p0171) which is new. The car is going to my mechanic today to sort out the throttle body bolt and to do a smoke test, so I should finally know for sure, but it seems like i have a vacuum leak somewhere.
     
  19. 00Mini

    00Mini Well-Known Member

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    Hopefully everything will end up being a fairly easy fix and you’ll be back on the road enjoying your car.
     
  20. trevhead

    trevhead Active Member

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    Update:

    The car has been given a thorough once-over by my mechanic at my request. Lots of good news and direction on what to do next:
    • Most happily, he checked everything I did, and all connections are solid and correct and completely buttoned up. Gave me an A+ and I can’t explain how relieved that makes me feel.
    • There is a vacuum leak causing a lean mixture that’s so minor it only triggers a lean code once in awhile, not all the time. Their smoke test found nothing. The only weak point is the broken bolt on the throttle body going into the intake tube.
    • They can’t drill out the bolt because it would ruin the brass fitting that it screws into, which is set into the plastic intake duct.
    • I’ve ordered a new intake duct, to arrive next week. I’ll put it in next weekend but in the meantime we all feel good about driving it safely.
    • Weird anomaly they can’t explain (don’t know how to feel about this): they don’t understand the low-ish idle. Their compression test read a shockingly low 60psi on all four cylinders. He said those numbers make them think it shouldn’t even start but that it starts perfectly, runs perfectly, and there are zero issues elsewhere besides the throttle body.
    I don’t know what to think about the compression. I still have a few things to do this weekend - I’m draining the cheap oil, installing the replacement drain valve in the oil filter housing, and putting on a slightly shorter belt on Detroit Tuned’s recommendation. But I doubt any of that has any effect on compression.

    anyway, this weekend will be filter drain valve and new oil. Belt if I can do it without pulling the bumper. If I need to pull the bumper for the belt I’ll wait and do that next weekend since I know I’ll do front end service mode to change out the intake duct.

    so close!
     

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