I'm with RustyRatRod on this one.
First , start the engine. go under the hood and rev the engine and look at the harmonic balancer. rev the motor to the rpm where you notice the shake. Is the balancer rotating smoothly or is there a wobble? Even a slight wobble and the balancer may be toast. Are you certain you have a correct flywheel for an internally balanced engine? How tight was the pilot bearing when you installed it in the crank? I'm guessing there were no issues with the drivetrain before you put in the 4-speed so the vibration is related to the crank, harmonic balancer or the flywheel balance.
