If the block is in the machine shop and you know you're going to use a manual trans, it's a good idea to see if the machinist can bolt the bell housing to the back of eh block and take a skim cut across the trans mounting surface. Of course, the back of the block needs to be set up for square (not just sitting on the front of the block). At that same time the trans index, usually the bearing retainer shoulder, can be checked for concentricity and adjusted. I've seen more than one hard shifting transmissions for no appearant reason. Good trans, good parts, good clutch...usually an alignment issue especially with aftermarket bell housing. Interestingly enough, this can apply to automatics as well. Not the shifting part, but just a good idea to check alignment. It's an extra step and takes extra time (and cost if you have to pay someone to do it) but can be well worth it in the long run.