One thing I learned the hard way, by destroying a case half because I was impatient, is if the gears do come off the transmission shaft pay very close attention to the direction which the gear faces on the shaft when you put them back together. There is a shoulder on the last gear that goes onto one of the shafts in a particular manner. One way it is correct and all will be good, the other it makes the shaft slightly longer than will fit between the case halves. It is not a big difference at all but enough to cause headaches and wreck things if you are impatient like I was.
The other thing I did wrong was to not know that if things are not going together smoothly and completely than take them apart and figure out why. If things are done correctly the shafts, bearings and case halves should go together with very little effort. (That is if you are heating up the bearings etc. to make the clearances easier to work with) When I did it incorrectly the cases were almost all the way together, very small gap left between them, and they just stopped moving, I just figured that maybe the bearings had cooled to the point of being snug on the shafts and I would use the hardware to snug up the case halves. Big mistake on my part. If everything goes correctly the case halves should pretty much fall together and the hardware will just be needed to hold them there. This is what happend when I got new cases and did it the second time LOL.
Hopefully my stupidity will save someone else from having the same issue I did.