[Joebie]

I haven't done a clutch job on my BMW but I did do one on my old VW Golf and the transmission mated up flush with the engine no problem.

I wouldn't force it with the bolts, there's gotta be something wrong going on in there. Sometimes it's hard for the input shaft to slide in the splines of the clutch disk unless you have the transmission supported just right but I've gotta assume you've tried wiggling it and supporting it as best you could.

Could it be possible that you got the wrong model clutch set or something? It's hard to give any advice beyond that without actually being there.

Good luck!