I found out 2 things while checking the stator bolt. 1 was that aluminum shears really easy, I know the because I sheared the stator bolt cover off the threads. 2 was that it wasn't the stator bolt. After making sure that it was tight, I started the bike and, although the knock didn't seem as loud, it was still there. I also noticed that while the bike was running, it didn't want to take fuel and the tach wasn't working, which leads me to believe thta I broke at least one belt. I'll have to do a complete tear down for sure now.
On a brighter note, I may be getting a replacement 1100 engine for nothing more than a solid days work and an 8 hour round trip. Still talking to the boss on that one though.