Spent more time working on the bike today. I adjusted the valves, intake were a little tight, and exhaust were spot on. Put some ATF in the primary and replaced the fuel line with clear that has a thicker wall than the stuff I was using that kinked. Also removed the chain guard because it was rubbing on the tire a bit and I need to make it fit better, and took the bike for a spin around the block. Unfortunately it was running on one cylinder again and it was pissing out the atf in the primary.
So I ordered a bunch of new seals for it and ripped the primary cover off. Once I got in there I think I found why it keeps running on one cylinder intermittently. The wire bundle coming off the stator was contacting the primary chain and one was partially worn through. I pulled out the clutch plates and they look good so that was the good news. There was also some water in the primary, I assume from me pressure washing the bike. Turned the ATF into a milkshake!
So to replace the seals on this side, the stator rotor and clutch basket have to come out. This will also give me access to the main shaft seal on the engine side so I'll be replacing everything. I also noticed while looking under the bike that these same wires coming off the stator exit the case and run down under the engine to the frame and it looks like they are also contacting the drive chain, so I'll be cleaning everything under the engine, removing the harness and I'll go through it to make sure all the wires are good and routed properly so this doesn't happen again. This could be the reason this thing was parked 40 years ago and never ridden again. :thumbup