Most liked posts in thread: 2004 R53 (re)Build Thread

Thanks - completely agree, I'm tackling one thing at a time. Starting with what I know, as you said - I'll address the obvious issues first. Honestly hoping I find a disconnected vacuum line or wire/plug... I doubt it, but that would actually be great to see something glaring like that.

The new intake tube arrived yesterday and I have the car back in service mode already. I'll probably get started with working my way down to removing the current intake tube tonight. Might end up pulling the radiator off all the way to make more space, I forgot just how tucked-in that intake tube until I really looked at it the other night after sliding the radiator forward again. No wasted space in there at all.

 

forgot to answer this... no, before starting this project, I'm pretty sure I had oil leaks from the crankshaft position sensor and the oil filter housing. Almost certain that there were no leaks from the oil pan itself and certainly not the main seal or the transmission.

I'm good to go on the CPS now, no sign of new leaks there. The bottom-most/hardest to reach with any tool bolt on the oil filter housing is wet and clearly leaking after removing the housing to put in a new gasket. I'm going to start by trying to get back there with extensions again and make sure the bolt is tight and properly torqued. Or, confirm if I managed the break the bolt.

The oil on the pan itself, and at the main seal area, is very hard for me to tell if it's even oil or if it's actually coming from the main seal mating point of the pan/block and transmission. I don't think it is because I can clearly see and touch seepage from up above that, on the front of the transmission, coming out of a mounting point with a bushing on it. That fluid is running down the front of the bellhousing, forming a droplet on the lowest point of that bracket, and then continuing to run to the oil pan, right at the seam between the pan and the transmission. At that point, maybe the main seal is leaking oil, and that's combining with the leak from the transmission, but maybe it's all from that leak on the transmission higher up.

At any rate, I don't think I had that leak before all this. I'm still concerned the raising and lowering the engine stressed the mounting points on the transmission itself to the point of creating new leaks.

 

Possibly/probably big news... BYPASS VALVE! It was stuck, jammed against a misplaced bracket.

Check this out. There is a black metal bracket that hooks over the intake side of the throttle body, two of the four throttle body bolts go through it. When I was doing the work the past several weekends, I didn’t pay attention to that bracket and where it was intended to be. I could have loosened it to get it out of the way, but instead when I pulled back the intake air horn to get the intake manifold out, I was pulling against that bracket. That bent it out of shape.

That’s important because when I put everything back together it was very much not in the right place. It didn’t align with the throttle body anymore, it was too high and angled too close to the intake for the throttle body bolts to mount through it. I left it that way because I was taking the car to my mechanic to deal with my broken throttle body bolt.

I think it wasn’t causing a problem yet when it got to the shop. When they got to that broken bolt and realized they couldn’t drill it out, they reassembled everything pretty much the way I had, only this time they managed to jam that bracket up into the plastic arm of the bypass valve spring housing. Tonight when I got to the BPV, I couldn’t press the arm in at all.




So, wow. This explains everything I think. If the BPV was stuck partially open, then the intake was getting the wrong measurement of air at all times - at idle, low speed and high speed. The way I’m thinking of it, this would be causing my lean condition and intake code. And causing increased fuel consumption as the computer made up for the starvation of air from the choked-off intake.

It was suggested at one point in this thread that I consider the Detroit Tuned bypass valve. At that point I didn’t even know what a BPV was, so thank you for suggesting it to begin with! (I think that was MCS02.) after researching what it does and watching ModMini’s video on replacing it, I ordered the stock BPV to just replace what I had because I remembered mine looking pretty scuzzy. Figured why not, trying to get everything back to good shape, may as well. New one just happened to arrive today, then I discovered the jammed up BPV tonight. Something went right again!

Tomorrow night I’ll start getting the new intake tube in place and attach the BPV and throttle body. Might get as far as being able to start it up. I bought a compression tester at Harbor Freight today, so I’ll test that when it’s running again and hope for normal compression again.


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Based on that explanation of when the BPV does what, I'm guessing mine was stuck nearly closed to maybe as much halfway open. My idle was the worst, but the car drove okay. Yet it didn't feel quite as good on the power as it did the first night we put it back together. The valve was just not situating itself where it needed to for anything to work quite right.

gonna struggle to focus on my work day the rest of the way today, ha. I'll dig in to all the new stuff tonight and maybe get it fired up again to see how it does.

 

+1,000,000

This has been my first real dive into Mini forums, weirdly, after 17 years of ownership. When I ordered the car back in 2004, I joined NAM right away and was active posting updates for whatever I learned as the car was built and shipped and delivered. I picked up the car in May 2004 and that was that. I just drove it.

It's only in the past two or three years I've started messing around mechanically with my cars. Mostly what kicked that off was buying a 2003 BMW 540 MSport in 2019. I bought a really good one but with the expectation and desire to learn how to work on it to keep it good. So I've been in the popular BMW forums quite a bit. They've been extremely helpful, for the most part. For the other part, I will say that community has a tendency to jump pretty quickly to answering posted questions with "That's been asked and answered a thousand times, just search" which is beyond frustrating. Not every issue boils down to the same keywords, plus forum platforms seem less-than-stellar when it comes to search. Case in point... this whole drama! I've had behaviors and codes and new parts, old parts, sporadic results... it sort of took living through it, thinking it out, writing about it, and reading (and re-reading) the replies here to make sense of it all.

So I came here for this project not really knowing what to expect, and I have been pretty much amazed. Hugely grateful.

 

Minor setback tonight but nothing too terrible considering the road I’ve been on so far.

That intake duct I ordered to solve the problem of the broken TB bolt turned out to be for an automatic Cooper S, and that matters... there’s a good three inches of additional tube between the bypass valve and the throttle body. It also places the throttle body lower.

Expert that I am, I discovered this after the nightmare of installing it... good lord. I wrestled and twisted and tore up my knuckles to get those vacuum lines attached to the duct and then line up the BPV with the air horn to reattach it to the intake manifold while aligning the duct with the supercharger... finally got it all to go and attached the throttle body and THEN I noticed that the bracket that holds the intake side of the TB down was nowhere near the TB. Laughable, I guess at this point.

I can’t get the correct intake duct for the manual here until next Thursday at the soonest. So I tore into that broken bolt in my old duct that was of course out of the car. Actually drilled right through it but the left behind junk of the remains of the bolt seems to be forever fused into the brass threads. So it’s a wreck. But I have a plan to rig this thing up and maybe, hopefully put it back together in “good enough” condition. I’m thinking that if I can get a slightly smaller diameter bolt that is also slightly longer, I can pass it through the opening with the leftover broken bolt junk and out the back where I can thread it into a nut and washer. Then I can have three good bolts holding the TB down the right way and this one corner kinda rigged up. I may add some gasket maker around the outside edge all around too but that feels like it could be overkill. If I can’t get a skinny bolt through that opening I’m going to go with gasket maker and, bear with me here, a zip tie to cinch down that corner into the gasket maker as tight as I can make it.

I want to get the car running so I can know if the BPV solves this whole drama. Then if I’m still having intake issues and I know I have this MacGyvered TB mess going on, I’ll order the new intake duct and do it again the right way in a few weeks.

Oh and I have some pretty troubling oil leaks going on for sure. Oil pan and oil filter housing are definitely leaking oil currently, and it’s looking like the rear seal probably is too. I don’t even know what to think about that, I just changed the pan and filter housing gaskets so if that didn’t solve the leaks and I just do it all over again, I don’t know that I should expect better results. But this time I won’t go raising and lowering the engine with the Jack under the oil pan and fresh gasket to do other work. Another problem for another day.


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Man, I needed that story. Brilliant. Absolute truth.


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Today's update. It's a head scratcher. Head shaker more like it.

I was successful with the tap and die on the intake duct, more or less. Got the old junk drilled out completely and new threads inserted. Test fitting the M6 fastener before reinstalling worked just fine. Everything went back together really nice and easy. Guess it's all that practice I've had recently. Only sore spot is that new thread isn't biting well at all. The M6 is threaded into it for sure, but I can't torque it. The TB bolts only torque to 7 ft-lbs, but before the torque wrench will click, that bolt has slipped out of the new threads. It's that feeling of tightening then popping loose, then tightening again. I just left it. I might take the TB out again tomorrow and see about rethreading the hole, or, doing what I mentioned the other night - getting a longer M6 and a nut. I actually like that plan better tbh.

I haven't put the front end back on yet, but I did reconnect the battery and cleared the old codes, and cleared all adaptations. To be certain, I used my Creator C310 to clear each adaptation individually, and then I used the onboard computer with the series of trip reset button presses and going in the coded menu there to run through the process described by Detroit Tuned in their instructions for their bypass valve.

The car started right up and, unfortunately, it sounds the exact same as it did before. It sounds rough, like it's missing. To my ear tonight, and who really knows if this is accurate at all, it sounds like the roughness can only be heard on the exhaust side. I don't hear the engine itself making any rough or missing noises. Because of that, I'm going to double check my torque values on the exhaust manifold. But it seems I'd have to have been pretty far off with those for the manifold to be loose enough to sound like this.

On the subject of exhaust - there is a ton of moisture in my exhaust. Ever since putting it back together the first time, after the cylinder head was off for a week, the exhaust pipes spit out a good amount of sooty water. I did keep the pistons covered with shop towels while the head was out. I know that condensation is normal, but it seems like a lot to still be in there. Although it did just sit for a week all over again, maybe it's normal.

No codes while idling in the garage tonight but I'm sure that's because it hasn't hit the criteria the computer needs to log a code, but I'm also pretty sure the codes will come back after a few miles of driving.

I do want to test the compression tomorrow. It will probably still read low since the idle is the same as it was. Then I'll put the front end back on and drive it and see what happens. I just don't know what else to do at this point.

 

Yeah, I got that bracket positioned properly, it’s attached to the TB the way it’s supposed to be and out of the way of the new BPV.

I’m going to double check the torque on the exhaust manifold fasteners today to be sure there’s not an obvious leak right there.

I’m pretty sure oil and coolant aren’t mixing, but I guess I won’t know for sure until I drain it the next time.


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Positive news. Car is running, and much, much better than a week ago or last night.

The idle is not quite right, still. There’s a miss to it. But, it’s significantly improved. All I did was take off the stock belt, which is supposed to be acceptable with the 2% bigger crank pulley and the 15% reduction pulley on the supercharger. But when I talked to Chad at DT he said that may technically work but that it should really have a shorter belt on it for that combo. I ordered it from him that day, about a week ago, and forgot to mention here that was going to be my last step. I didn’t expect it do anything but I wanted it to be the right tension.

Shorter belt, smooth idle again. The difference is in the elimination of the low, deep resonance that didn’t sound right at all. Now the idle frequency sounds right, but it has a bit of fluctuation to it that doesn’t sound normal. So much better though.

My son has the car out now on his own after we drove it together for awhile. It feels zippy and powerfully again, so things are looking up.

However... after the drive, it had a code for the old Misfire Cylinder 2. No SES light though (although the ASC light comes on and stays on, which it does when overboost is detected. What I’ve read is that will be normal from now on thanks to the reduction pulley causing boost beyond what the normal R53 computer is programmed to call normal.)

The misfire is likely what I hear at the new and improved idle. Driving is basically perfect. Honestly it felt pretty amazing again while driving today, so that feels great.

Didn’t do the compression test, my son was pretty antsy to get the car out to see some friends and I was out of energy for one more thing to do anyway. We’ll check the compression at some point this week and have more data to go on.

Not sure how seriously I should take this misfire. I want to find it. All this work just to cook the cat or something like that by ignoring the obvious would be ridiculous.

Getting there!

 

I'm about at the end of my rope. As of yesterday, the car is behaving the exact same way as it was when I first posted here back in January in a different thread about the misfire on cylinder. Yesterday afternoon, it did everything all over again that it did in January:

• cold start, SES blinked
• engine turned over, revved up to about 1200, stayed there, then dropped
• idled rough as revs fell under 800
• engine died
• waited a moment, cranked again, started up fine, no blinking SES. idling at 800-900 as it did on Sunday, sounding good except for an audible miss
• trouble code for Misfire Cylinder 2

Exact same behavior it had when I embarked on this whole thing, which is now feeling like a fool's errand. This is what led to the diagnosis of the burned valve on cylinder 2. Which led to the valve job. And everything else documented in this thread. And I'm back to zero with this thing.

Last night I was becoming convinced that the misfire and the low compression on all four cylinders was a timing issue, and that I messed up the timing with the new timing chain. Even though I have a photo of the chain, lined up properly to the arrow on the cam sprocket and to the two arrows on the crank sprocket, taken immediately before I reinstalled the timing cover. But that's not it, it can't be, because the engine is doing exactly what it was doing before I ever touched the timing chain or even looked at it.



I think I have time tonight to pull it back in the garage, on the ground not stands, and at least test the compression to confirm for myself that it is in fact still running very low compression. I plan to do dry and wet on each cylinder so I can get all the data I'm capable of. Question of course is, then what... say the compression is still low. Okay. Cylinder 2 is misfiring. Okay. What do I already know about that... the injectors were resealed and bench tested and passed. Cylinder head is machined and there are no signs of leaking anywhere around the seam/head gasket. I have brand new NGK plugs installed (cooler ones for the added boost). Ignition coil and wires didn't affect anything when I swapped my new-ish ones for brand new.

I haven't done anything with fuel delivery yet, i.e. fuel filter and/or fuel pump. I probably should.

I'm circling my mind back to where I was a few weeks ago thinking about everything I changed/modded at the same time, wishing I'd done things one at a time. The crank pulley feels like the outlier to me. I've put on this super-lightweight 1 lb non-dampened crank pulley. Changing the belt length on Sunday by 15mm (I think that was the difference) significantly changed the idle. Stands to reason that a different crank pulley would too, even though Chad at DT who I trust told me it won't. It has to, right? Different mass completely, in a big way. Old tired out engine. I'm thinking about pulling it and putting the stock pulley back on, cracked dampener and all, just to start it and see if it's different. Then buy the PRW crank pulley and put that on if it runs better with the old stock pulley back on. I'll need yet another different length belt to do that but at least they're cheap.

Guess I'm rambling now. I'm out of bullets. I've managed to fall down the rabbit hole of a many a DIYer I guess, spending a few grand and a month of weekends in the garage and I know exactly what I knew about these problems when I first showed up. Misfire, bad idle, engine dies sometimes. Although I've learned about working on the car which is cool. I just have to solve this.

Freakin A.

 

I've been quiet this week, didn't touch the car until today. I promise I won't leave loose ends with this and will continue to update as I go, and hopefully end up with a resolution. No such luck yet today.

All I did today is check the compression myself for the first time. I drove the car first to get the temperature up to normal operation temp. When testing compression, I unplugged the coil pack, removed all four spark plugs and cranked it with the accelerator all the way down until the pressure gauge stopped going up. I read averages of:

1. cylinder 1: 137 psi
2. cylinder 2: 127 psi
3. cylinder 3: 135 psi
4. cylinder 4: 130 psi

Pretty far from the 60 psi my mechanic got. There's no way they did that on a warm engine. They must have checked it when cold, probably because I was telling them that the misfire and rough idle was only on cold startups. But more accurately, the idle is rough and missing regardless of engine temp. Does it when cold and when warmed up. Everything is still great under power, but as soon as the car stops, the idle is rough and audibly missing.

Also, I had it in my head, somehow, that this engine's normal compression is 90 psi. I went to double check that as soon as I read cylinder 1 at 140 (first reading), and now I'm only finding references to the R53 having normal compression anywhere from the 150s to 170s. Appears I'm low, but not insanely low like I thought. That cylinder 2 is the outlier though, and that's where the misfire code continues to be focused.

I'm nearly out of ideas. I could go chasing more of the fuel delivery system, like the fuel filter and pump, but those wouldn't have anything to do with a misfire specific to just one cylinder. All I can think of right now is to just focus on the basics - air, spark, fuel. I've dealt with air - fresh valve job and no more vacuum leaks. I've dealt with spark - brand new, cooler NGK plugs, and confirmed that my coil pack and plug wires are good (based on putting in new ones that didn't change anything). Fuel is all that's left, and in my mind it's all down to the cylinder 2 injector now. Even though my mechanic bench tested the injectors and told me they are fine, I'm going to try swapping injectors between cylinder 2 and 3 or 4 to see if the misfire code moves with it. I should have done that first, and I feel like it has to be that injector. I don't know how else to explain the persistent misfire on cylinder 2 after everything else that has been done.

In other news, I'm going to cut bait on the 2% undampened pulley. I bought the PRW and will put that in assuming I solve this misfire soon.

 

This is the plan for tomorrow - fingers crossed that a few more hours of diagnosis and swapping parts around will reveal the problem and solution!

Thank you all for the help and advice, Lee especially has been awesome!!


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