You said,"I don't think it is balanced the same with the heavier piston. How could it turn 1k more RPM??? Any ideas"

Try the newer piston and rod in the older setup. You may be able to loose some of the vibration.

If it still vibrates to much, then run a bigger prop to slow the engine down.

Does the older engine vibrate a lot at mid-range or just the upper RPM?

Look at the difference in the port size, the older one simply had bigger transfer ports.
Bigger ports means more HP and RPM if the port timing is the same.