I actually just stepped in from my garage while doing this same swap. you have to use the m3 driveshaft since the diff is longer on the m3. so the diff to center bearing will remain unchanged from the rear end. and then you have to get the front end of the driveshaft modified for your 5 speed tranny since it is shorter then the m3 tranny. ALSO! and i just made this mistake and I am furious because of it. The flange on the 6 speed bmw trannys is different then the output flange on the 5 speed trannys. It is larger. therefore when you are getting the driveshaft customized, u must also transfer the flange off the 5 speed driveshaft to make it work. I just spent hundreds of dollars on customizing my driveshaft and made this mistake.
little bit of a threadjack but it will come to your benefit knowing aswell possibly, but would the m3 transmission output flange bolt onto the 5 speed because I know it is held in by 1 bolt, the only reason I havent gone forward and checked is because I do not want to bother sourcing the flange if it might not work. the shaft coming out of the flanges are the same, but is the shaft inside the transmission actually the same. If anyone could answer this that would be VERY greatly appreciated.