Alright, but what if the gaps are the same. I did this last weekend, had a few buddies over, and the gaps were the same all around, but no progress. Input shaft and clutch splines were aligned. Should I take the clutch off and check pilot bearing fitment again?

Since you have verified everything else; did you confirm the pilot bearing is seated properly in the recessed area of the crankshaft ?
 
Alright, but what if the gaps are the same. I did this last weekend, had a few buddies over, and the gaps were the same all around, but no progress. Input shaft and clutch splines were aligned. Should I take the clutch off and check pilot bearing fitment again?

If you can't get it to go together, I don't see any other choice for you but to pull it off and double check the fitment of everything. make sure you don't have any burrs on any of the mating surfaces. From the looks of your pictures the input shaft is close to if not starting in the pilot bearing, you could have a burr on one of those.
 
If you can't get it to go together, I don't see any other choice for you but to pull it off and double check the fitment of everything. make sure you don't have any burrs on any of the mating surfaces. From the looks of your pictures the input shaft is close to if not starting in the pilot bearing, you could have a burr on one of those.

Alright, I'll pull it apart and check fitment tomorrow. Thanks!
 
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When I had issues mating my engine to manual transmission, a buddy of mine suggested that I put the transmission in neutral. It definitely helped the splines line up and I also used some long bolts with the heads cut off as guide pins. It took a little bit of shimmying and shaking but I got it back together by myself. The first time I did it went smoothly but the second time I swapped engines I put a motor mount lift on so it made the angles different and therefore more difficult.
 
When I had issues mating my engine to manual transmission, a buddy of mine suggested that I put the transmission in neutral. It definitely helped the splines line up and I also used some long bolts with the heads cut off as guide pins. It took a little bit of shimmying and shaking but I got it back together by myself. The first time I did it went smoothly but the second time I swapped engines I put a motor mount lift on so it made the angles different and therefore more difficult.

It's not in neutral, but the splines are all lined up. I turned the Enfield over by hand rather than the transmission, so I'd know when it like up because the vehicle would try to move when I turned the engine.