Well I bolted the flywheel up to the motor and spun it up. What a difference! The wobble was almost entirely gone. There is still a small vibration at around 500 rpm while the motor spins up, but when the RPM's climb just a little higher and beyond, it is as smooth as glass.
Now I just need to get the pressure plate mounted back up and start re-assembling the drive train. Mounting the pressure plate is going to be tricky as it is naturally sprung to push on the clutch disk, meaning I have to collapse it about 1/2" to get it on. When it's new it has a retaining system that holds it until you bolt it up, making it easy to get it on the flywheel. Well, that's gone so this could be tough.