I've never done a clutch, but I'll take a few guesses. I'd think the flywheel was OK if it worked on your M40. There isn't any difference between them as far as I know.
You used a centering tool on the clutch plate, right? It's a temporary plastic plug that ensures the clutch plate is centered between the pressure plate and flywheel.
The flywheel was put on the motor with the correct centering sleeve, right? One of the flywheel bolt holes is machined slightly larger - it matches one of those holes to a wider hole in the flywheel. There is a hollow sleeve that keeps the flywheel locked to the crank in the proper position. It's part 3 on this diagram:
http://realoem.com/bmw/showparts.do?model=AJ52&mospid=47273&btnr=11_4358&hg=11&fg=20You might also want to check part 5, the centering or 'pilot' bearing for the gearbox mainshaft. It's installed in a recess on the rear of the crank.
Did you replace the clutch fork pivot pin, right? It's part 5 in this diagram:
http://realoem.com/bmw/showparts.do?model=AJ52&mospid=47273&btnr=21_0011&hg=21&fg=05I'd also be interested in the vibration damper, but I'd suspect it's a low probability failure. That could be cracked, etc. I'm with you though - if the car didn't vibrate, then had a clutch failure, I'd suspect the clutch assembly. I've never seen a melted throw-out bearing - was the transmission input shaft, main bearing or front main seal damaged?