Well Cat was supposed to respond to this thread last night and save you guys a bunch of time. But we got the bike running after figuring out what was a really stupid problem. We are getting this 550 engine running in its original chassis which is a 77 K model that is really beat to #$%* but 90% stock. And when the engine is running we were going to pull it to put it in a 500 chassis. So really all we wanted to do was confirm it runs before we move forward on the project.
Anyways, we swapped the coil leads for 1 & 4. Didn't do anything else besides the valve adjustment the night before, but all valves were close to spec. Not sure what that helped but now the bike was running on all 4 cylinders. It was still running weakly on choke only, though.
Since we are planning to pull the engine the chain and sprocket are removed as well as the sprocket cover. As we had it running I noticed the sprocket shaft is spinning really fast. So I stick my foot out to stop it and it's not stopping. So we shut the engine off and it is in THIRD gear. This whole time, lol. We put the gearshift lever back on and shifted to neutral, and it ran fine, no choke. It revs up and returns to idle. It will need a carb sync, but that's all. There is also some puffing from the carbs when you crack the throttle, but I think that can be fixed when the airbox is installed and air screws adjusted.