1989 Ford Mustang Engine vibration

I have a vibration that is comeing from my motor. I know its motor related because it does it when you are sitting still as well as when you are moving. It was originally comeing on around 3000 RPM's. I pulled my tranny out and supported the rear of the motor and tightened the motor mounts back up and started the car and reved it up to 3000 and higher and you couldn't feel it no more. I put my tranny back in and you could feel it again. So I pulled the tranny back out and I put a fresh one in that had 0 miles on it that a friend just bought and same deal you could feel the vibration with his too. This vibration is bad enough that it will vibrate the shifter so bad that it hurts your hand and arm to hold onto it. My flywheel, pressure plate and disk, pilot bearing all look fine. I just put this motor in 2 months ago after it was freshened up. It has roughly 2500 miles on it. I did find that the weight on the back of my harmonic balancer was lose. I tightened it back down and started the car up and the vibration was gone at 3000 RPM's, but now its at 5000 RPM's. Not sure if its something inside the motor or not but I need some advise here before I start to tear my motor apart. I have thought about a miss from a burnt plug or something but when you rev the car it doesn't act like it has a miss. This whole deal started all at once it didn't gradually come on. Last Monday the car was fine and Tuesday morning when I started it, it was doing this dumb stuff.