That e39 subframe will not fit in an e46. You will need to go with an aftermarket lsd unit for the e46 non-m carrier or get an m3 rear subframe and diff assembly. If you go the m3 subframe route, you will need different rear wheels due to a change in offset.
I believe that the m3 suspension fits if you knock the alignment dowel out on the front strut towers. i cannot confirm for sure though.