Thank you guys for the responses.
Laitch: I don't know what "out of phase" means...
It is definitely the engine causing vibration, pull clutch and there's nothing while rolling. Synchronizing is due once I have her back together. It's going to be a while. Pulled engine apart, was shocked about gaskets and seals and head gasket prices, spent $ 1500.- so far. Wear is marginal, rod bearings are hardly run-in. P.O. must have done oil changes regularly. I only used synth oil, seems to be doing good. Rubber boots on intake look fine, so do the plastic connections. On re-assembly I will check valve play, make sure mechanically everything is good there there. Right now cleaning pistons and going to check their weight (balance). Have to wait for ordered parts to come in. Then I will be working again with little time for wrenching. Took 2 weeks off to work on bike, not nearly enough time...