Got the stock clutch kit, soaking the plates in oil. Figured I would start it up to warm up the oil before I drained it. Tank on, fuel connected, gas On. Bike fires right up, runs on choke for about 20 seconds and then I take it off choke to let it warm up. Raise the idle screws by half a turn each and pull in the clutch. As you all suggested, all the noises went away. Most of the clunking sound was coming from the transmission, as soon as you pull the clutch in they went away. Then bike dies. Huh. Check over stuff, make sure I didn't forget anything, fires right up again, got the idle set at 1300 rpm. Then dies. This repeats for several minutes. Finally I switch to reserve on the petcock. Runs fine. I guess that is what you get with non-OEM stuff, have to find a petcock that works. Also thinking if it is limiting fuel at idle it could be why it doesn't run consistently when I ride it.
This build started out as an exercise in design and fabrication and has turned into troubleshooting every component of a functioning motorcycle. Anyone have an extra 76 CB550 petcock lying around?