Yep the crank job is quite specialized because its got to be pressed it up to have recommended conrod side clearance & it's easy to go to far & not easy to get it perfect when doing a home job without good gear--like i haven't got!!. Also, & just as important, or more important, is truing it all up so the crank spins true.

oh god is there another special machine for truing a crank... probably haha. Only thing I've ever trued is a bike wheel, guess I'll start looking for motorcycle shops nearby

Alright, I replaced the lower end crank bearing along with all other bearings inside. Put the case back together and now I'm running into issues on the clutch side. As shown in this video  www.youtube.com/shorts/goK09__uWUs I could get it into all the different gears by hand, but when I attached the gear-shifting mechanism it only grabs like half the time and I can't find neutral. This is all new to me so sorry if its a simple fix. I put in the neutral switch ball and spring which was one of the items that started this whole thread in the first place. What am I doing wrong? or did I assemble the shifting forks on the transmission incorrectly and will have to split the case again? Any advice is appreciated!!! 

imgur.com/a/du6uKWo

Check alignment on the selector arm. It should be centered on the selector pins. Have to do the check in 2nd gear or higher. If it’s off center you’ll need to adjust the arm with the eccentric adjuster at the bottom of the arm near the  right bottom of the clutch basket. Should be better instructions than mine in the forum or within the service manuals on this site. 

Here's a video on how to adjust the shift arm that ADGUY was talking about:

adjusting shift arm

Have you got the selector drum retained over to the left with the parts under the three screw cover above the sprocket--was just a thought. You say 'neutral 'switch' ball & spring. i'm sure you mean neutral position finder--as i call it. Neutral light switch should be there too beside it if i'm thinking right. Sorry just want to be sure. Ball & spring should hold it solidly in neutral. Adjustment should be ok if it was ok before, but if it needs changing then follow ADGUY2112 advice above. Also, trying to go through all gears on the bench will only work if you revolve one shaft a bit to align the dogs for each gear. Just forward & back an inch or so for each gear to slot them in.

Yes, must spin the shafts! They can be difficult to shift on the bench.

Thanks to everyone for the quick and detailed responses! I solved the issue with the transmission and got everything in working order with help from that video and all of your advice. I got the bolt that was seized in my armature out but now I can't find the woodruff key for that side... damn.

more issues are that when I tighten down the primary drive gear the crank gets very hard to turn. At certain tightenness points it feels like it binds up or catches when the connecting rod is at TDC or halfway down, seems to change quite often. The only thing that seems to fix this is just having it loose... but that can't be right. Any ideas what this could be?

Did you forget the crank shim?

Just went through all my leftover parts... you would be correct. Totally forgot to put in both sides. Seems like with anything I do for the first time in the automotive world I end up having to take everything apart again and put it all back together. Not that upset with myself as I bought an extra set of crank seals for if I screwed something up along with the fact that I basically had everything assembled again I now know *more* of what I'm doing and can hopefully put it back together much better than this first go around