Sorry, I failed to specify I was using an actual Muncie shifter along with Muncie linkage. All is new, so it should work as intended. I was able to use a feeler gauge, as the alignment hole is flat. I was able to get 1 thru 4 gears lined up and it will go into reverse, just really hard to go over and up and once in reverse, it wants to stick in reverse. Thoughts?

Also, the output shaft will still turn while the trans is still in neutral. I don't have driveline hooked up yet, so can't tell if I would be able to stop the wheels with my hands. Is this normal? This is a newly rebuilt trans with new bearing, clutch and flywheel, if that makes a difference.