So on swapping my motor I found that the rear exhaust gasket is totaly trashed (the one about 10" off the rear header). I am wondering if this could be enough air leak to cause the bike not to run properly, or seem like one cylender is not working. It shouldnt but with no back pressure it cant be good...

 

Geekonamotorcycle was having exhaust issues similar to this and they caused him to run rough with lots of popping. It didn't cause smoke for him I don't think, but replacing the gaskets helped. I don't know the full story and can't quite find it, but here's a start:

https://www.superhawkforum.com/forum...-advice-25246/