Steve..The gear usually bottoms on the circlip and ends up slightly proud of the end of the shaft splines to give a larger bearing surface against the face of the bush. Ideally you will end up with both the face of the gear and the end of the splines dead level to give the maximum bearing surface to the bush. Mainshaft endfloat is controlled by the ball race in the inner cover, so should be none existant, only the lateral slack in the bearing.
As duTch says the thrust washer goes with the internal chamfer towards the clutch. Look closely at the layshaft, there is a nice smooth transition in diameter, the chamfer clears this. Aim for the smallest possibe endfloat, even grinding down the thrust washer thickness to achieve the best result.
Layshafts usually end up with scoring and damage to the blind bush contact area, so the usual fix is a new, expensive layshaft, a better used one, or get the damage ground off and obtain a custom bush with a smaller ID to fit. If you are lucky and the shaft is reasonable, a new bush may be all you need. Unsupported at the timing side end, there will always be little waggle to the layshaft. It is the excessive running clearance that causes the problems of noise and vibration.
The bush is best removed by heating up the case, oven, camping stove etc and knocking it into the case with a flat bottomed bar drift . Freeze the new bush to aid installation into the hot case. Make sure the oil hole lines up. The bushes tend to close up once installed, so now the layshaft will not fit. You may be better off getting a package deal from you local machinist, reaming a blind bush at the end of the case is a pain. Otherwise the emery cloth on a round dowel trick as extolled by duTch. ( A very clever fella if I may say so).
Swarfy