Greg... I've been messing with these transmissions for 50 years. Mostly 3100's.
Yours is a simple swap. You say the teeth on the "new" flywheel are good... most any automotive shop can flip the ring gear over to use the teeth on the other side if needed and I recommend having the flywheel resurfaced. Replace the pilot bushing in the end of the crankshaft, as a worn bushing will enhance its ability to jump out of high gear.
Your bad transmission has the perfect alignment tool... remove the input shaft and use it for alignment, bearing and all. I made two bolts with heads cut off into alignment studs, one 3" and one 4" long with a screwdriver slot cut into the end so you can screw them back out of the bell housing. I slide the shaft into the throw-out bearing, line up one stud to the trans, line up the short stud and slide the tranny on. Start the two lower bolts, remove one stud and start that one etc.
