Hi Robb, end float on all shafts is 005"-010", aim for 005". As Ian has said before there are plenty of working boxes around with greater end float than this but you want to reduce the loss of movement when selecting gears.
Shims are placed under the flanges of the bushes at either end on both the lay and selector shafts. The shims can be steel or brass.
For the main shaft shims need to be steel and are placed on the sleeve gear between the pinion and the oil retaining washer. At the kick start end between the distance washer and the oil flinger.
Lastly if you're making your own inner cover gasket make sure you cut it from the thin gasket sheet 0.4mm I think.
Hope this helps.
As Matt says you have to consider the thickess of the inner cover gasket. If you have a 'thick' gasket you can use it but will simply consume more shims when settig the end float.
I recommend shimming each shaft individually before replacing the complete gear cluster into the box.
Don't forget to use a 'dry' inner cover gasket when doing this...Ian
What you can do is press the bush into the gearbox just a fraction to reduce the clearance, if you only need to lose a few thou, as the gears are straight cut it would not move, or you can remake a bush with a fatter flange to compensate for it.