=> Please note <= I'm not taking those pesky shafts down to component parts. There are checks to be done on the synchro parts - there are wear limits that should be checked. Like I said I'm not bothering - I'm taking a gamble - I reckon I got a diamond here. It'll be alright - it'll do a trip!
{This could bite me on the arse of course}
So assuming you've checked and re-assembled the lay shaft and the main shaft and it is all good...
...it is worthwhile making a few measurements to make sure that the bearing clearances are good.
The first thing that can be done is to check that the main shaft is at the correct height with respect to the intermediate plate.
Looking back at the specifications listed above it should be 138.4 mm
Spin the main shaft around on its taper roller bearing whilst it sits in the intermediate plate cup. Try making measurements at several points on the casting. Ideally you need a bigger foot on a depth gauge than the one I have.
This dimension is adjusted by changing the shims under the bearing cup in the intermediate plate.
Note that the bearing cup for the lay shaft has NO shims!