if you only have small changes to make then it often depends what shims are there already and what's easiest to change.
if you want to get really carried away (or if someone has f#%ked it up before you got there) then you can fit the gearbox shafts, shift drum and shift forks. without the crank in you can get in thru the cylinder holes and check the sideplay of the shift forks as you go thru the gears. that way you can see if anything needs to be moved in a particular direction.
on the 750 i'm putting in my 600m i had to do this as the lh input shaft gear (2nd?) was hitting against the sprocket bearing lock plate and had previously been rubbing on it - it's been apart before. so i had to move that shaft to the right quite a bit and also move the output shaft to the left from memory. so i then had to move the shift drum to make sure it shifted nicely, as it was not getting into a couple of gears.
actually, now that i think about it, i had to move the input shaft for clearance, the shift drum to work with one of the input shaft gear selections and then the output shaft to suit the new shift drum position.