"when replacing a gear you put the two halves of the needle roller cage on to the shaft first and then place the gear over them..... so what's the trick?"
thick grease will hold stuff in place during assembly
Some other trans assembly tricks
When installing the two shaft assemblies into the case or case half, we're talking the input shaft and the counter shaft with all the gears installed, set them together on the bench and tie a shop rag around the center to hold them together and in position for assembly.
when assembling gears on shafts hold the shaft vertically in a vise using cardboard or brass jaw covers to pad the vise jaws. I even have some aluminum padded vise grip jaws.
Always use brass hammer, brass punches and mallets when working on tranny's, never a steel hammer.
You can use a press to assemble and disassembly shaft assemblies when necessary but sometimes it's easier/quicker to use a brass punch, bet never pound on gear teeth edges, always at the base of the gear.
Be careful of gear teeth, while they are very hard they are also brittle and can easily be chipped, typically when prying with a screwdriver. If you do get a small chip it doesn't necessarily mean the gear is junk but it will cause a tic, tic, tic, when the tranny is spinning. You can fix this by using a carbide bit die grinder to take the sharp edges off the chipped area.
After the case halves are put together, hold them together with about 3 bolts and bench shift the tranny running through all the gears and spinning the input shaft while watching for correct output shaft operation. It's easier to check at this point than after the trans if fully assembled and installed in the vehicle.
You can be tricked at this point if you've got a syncro that's was pushed hard onto a gear during assembly. The trans will seem to be locked in gear when it's in neutral. You have to apply a moderate amount of twisting force on one shaft while holding the other stationary to break the syncro loose. You can avoid this by making sure the syncros are all loose right before assembly.