Over the years, I have done hundreds of clutch jobs, FWD,RWD, 4x4 and AWD, and I have never had to use the transmission bolts to "pull" the transmission into the bellhousing, provided the clutch disc is properly aligned. I have seen far too many Muncies, T5s, and even the occasional Toploader that had one or more mounting ears broken off from this practice. I rarely use those cheap plastic clutch aligning tools that come with many clutch kits, they are just too sloppy fitting. I have a good steel universal alignment tool, but for my Toploader/Jerico/GForce, T5 stuff, I have old factory input shafts that I much prefer. Even if the transmission case doesn`t get damaged, by using the bolts to force the transmission into place, chances are the clutch may chatter, due to bending or distorting the disc. If everything is aligned correctly, the transmission should slide in all the way with no force.