The tranny poping out of gear is a worn tranny issue.. should have nothing to do with the rebuilt engine.
Also.. the tranny won't have much effect on hard starts unless the tranny countershaft was binding somehow.. and you don't press the clutch before starting it. Pressing the clutch is a good idea. that way the starter doesn't have to turn over those extra shafts, gears, and that heavy tranny oil.
Early 8n's used a front mount distribuitor.. and a 4.5v coil disguised as a 6v coil To get away with this they used a ballast resistor with a variable heat coeficient. When the tractor is cold, the ohms are low on the resistor.. it lets more votlage thru to the coil.. once the resistor warms up ( minutes ) the resistance goes up, and drops the votlage slightly.
Average to good voltage ont he primary of the front mount coil is battery volts with points open, and a minimum of 2.5 to 3.5 volts ont he coil with points closed. more than 4v will cause coil and points damage.
Some well meaning shade tree mechanics bpass the resistor and then slowly cook the coil and points.
Hard warm starting is a sign of a bad coil, though could also be a bad ignition switch.. ford had very weak ignition switches.
Use a jumper wire and bypass the ignition switch next time it is hard to start. If that doesn't help.. replace the coil and the resistor and points.. or at leas the coil and clean up the other connections and wireing.. Points can sometimes be polished by taking a piece of brown paper bag and pulling it thru the contacts while holding them closed multiple times. Unless you have a real 'ignition-hone' don't try to file your points.. plain bastard files and emory paper are very bad for points. Besides contaminating them, they leave the surface too rough on the microscopic level. Ignition hones are much much finer files.
Soundguy