Did you clean out the gas tank? There will be varnish within it. I'd suggest
Techron, or some other uber-strong fuel system cleaner (
SeaFoam won't be strong enough, for this application), and put it in, full-strength, seal the tank, then swirl it around for a minute. Let it sit for 10 minutes, then repeat, and drain it into your car's gas tank (near full, to dilute it).
When you get it running, I'd suggest using
SeaFoam in the crankcase: add the proper amount to the oil, start it up, and run it on a short ride (shift through all five gears!), until the engine is warmed up to an oil temperature of 180 F, or higher (5 minutes, minimum), then drain the oil, and change the filter -- it should be coal black, with carbon, and varnish deposits which are suspended in the oil, having been flushed out of the engine, and the transmission. You won't need to do this again, for at least 20,000 miles, maybe more, if you use a modern (SM or higher rated) oil, as they will keep everything pretty clean.
That bike really is a time capsule. Thanks for sharing this re-build process with us. Cheers!
1979 CB750K (sold, 2012, but not forgotten)
1983 Kawasaki 440 LTD Belt Drive (sold, 2011)
1993 Kawasaki Voyager XII