I have a lead on a low mileage used JCW engine complete with supercharger, transmission and ecu. The car it will be going into is a 2002 MCS. The used engine/trans. assembly is out of a 2003 JCW. So, anything I should need to look out for when making the swap? I am sure it has been done by some one here already. Any pitfalls/roadblocks I may run into seeing it is not an engine from an MCS? For information sake, the engine coming out has a very weak #2 cylinder. Heavy misfire/undriveable. Only 80lbs. of compression. That is the reason for the swap.
As long as your swapping you should add an LSD. With the JCW set up you can quickly generate more power than the open diff and tires can handle. From what I've read the main difference in the first gen motors is the head, sc, injectors, cat back, and intake. So there shouldn't be anything that would be wrong physically. The ECU may be a different matter. I think it has to be matched to the body control computer. But I'll let others that more than me chime in.
Make sure you get the BCM and ECU and you my need the ignition key cylinder so everything is coded correctly. FYI your VIN will not match for emissions, if your state has emissions.
Looking back at some of the information I received it says that the engine comes with the "ACC" and "EBX". Now, I think the ebx is the engine computer. Is the acc the body control module (Accesory Control Computer...???)?
If I remember correctly, the engine computer between the Cooper S and the JCW is just programming. The dealer simply activates the JCW profile on your existing ECU. In 2002/2003 the JCW engine was a retrofit. That means, you buy a Cooper S and the upgrade was a dealer install. The kit included supercharger (reduced pulley and teflon bades), engine head (ported and possibly a different cam profile), exhaust, and a different intercooler cover. Other options would include suspension (red springs) and struts, as well as a 2 piston brake kit. The JCW brakes would become the standard brakes for the R56 generation.
From MotoringFile: MotoringFile » Archive » The History of the Modern JCW Tuning Kit If you look at RealOEM.com, you don't see an ECU in the JCW parts package, so I think it's just a software reflash at the dealership. RealOEM.com  BMW R53 Cooper S JCW Tuningkit 210 HP RealOEM.com  BMW R53 Cooper S JCW Tuningkit 200 HP
You can't put the used ECU in your car as it won't work with the other computers. But you can put the JCW flash on your existing ECU. If you need you can ship your ECU to us and we can put the JCW flash, or another tune on it for you.