i'd renew the oil seals in the crank eg clutch and output shaft.
I use wellseal for the halves
check the "dogs" on the gears for rounding off as they will slip out of gear under power.
Chipped teeth on gears.
clean the gear bearings with cleaner and spin them, if they make a "shhh" noise they are fubared (sic!) (usually ok as they are in oil)
check the needle bearings for wear.
have a look at the selector drum and for bent/worn selector forks
check scoring on mains if you have them off, rubbing marks are ok
check con rod movement as per manual
get the cases vapour blasted if its all out as this would be the last time you will hopefully do this.