Just make sure you do a dry-fit first. Double/triple check the bearings to make sure they're properly seated on the locating pins. People have cracked their cases because they missed that and forced the cases together.
Should basically take no effort to have the cases completely closed. The nuts should not be used to actually close the cases.
Double check for the thin shim at the end of the transmission shafts - sometimes it is missing. And if you've got $50 burning a hole in your pocket put the taller 5th gear on if you haven't already. This is your only chance to do that.
You've clearly replaced all the seals?
The shaft for the starter motor is back in place? Make sure you put the retaining clip on the side to keep it in, as otherwise the shaft can slide back out and drop the large gear off inside your engine - then you're opening it up again.
Oh, and put on your 'double check' list for the top end to make sure the little oil baffle metal clip is in the head. I forgot mine and had to re-do the top end, replace the crushed head gasket, re-do the Yamabond etc.