On the E39 M5, BMW M specified 800-1000 gear changes under "normal, moderate" driving conditions yields an optimally broken-in clutch/pp/flywheel. This was derived through empirical testing. I would hazard to guess that a similar experience is valid with the new M3.
See this post.
2011.5 M3 sedan 6MT, Silverstone, no sunroof
2001 M5 LeMans Blue/Silverstone
2006 330i 6MT Red/black, ZSP, Nav, etc.
2001 Audi S4 6MT; 1996 Volvo 850R wagon