Engine vibration.

[98 hoe]

Hey guys few quick questions. I got a Nasty vibration in the car right under 3000 rpm and up to any where from 4500 to 5000 ba enough to scramble an egg. At first I thought tires but I balanced them and made no difference. Then I noticed that if I am parked and in neutral slowly bring up the rpm it starts to shake so I know it's not a wheel tire o tart end problem. I have come to a few possible conclusions. 1. When I put the balancer back on I didn't have cylinder 1 at tdc compression. 2. I had the flywheel machined maybe that's off a hair. 3. I did swap cranks when I built the motor and it now I realize that the crank I put in was from an automatic and I have a stick could that be a problem? I am looking at a new balancer that is keyed so I know it's on right. Any info or ideas would help thanks.