Ok I don't know if you have the same problem that I figured out on a customers truck.. But anyways
The customer came in with a '93 S-10 4x4 for a transmission. I also noticed it had a terrible terrible vibration. I found out as I was removing the crossmember that it was bent up so far that the top of the transfer case was against the trans tunnel in the truck. I bent the crossmember back to original and the vibration was gone.. Maybe just make sure that yours isn't like that and also check all the motor/trans mounts to make sure they're not wrecked