Okay, well, since the vibration quit when you pushed in the clutch, and it still vibrates in neutral, I think you can eliminate any gear damage to your tranny, your flywheel, pressure plate and your driveshaft.
What you can include is your input shaft, your clutch disc, and your throwout bearing.
My best guess is that a piece of your clutch disc is shredded, which is throwing it out of balance, kinda like a tire that is missing a wheel weight. I just can't see the throwout bearing doing that, and I'd like to believe your input shaft is still good, although it would also be likely to cause the problem.
If I were you, like
smithbling says. Check out the front of the motor, just in case. It's wishful thinking, but why not? It'll only take a minute to pull the belt off. When you do, just run it up real quick to the 2800 or so, and if the vibration is gone, put the belt back on, if it's back, your problem is up front.
It that proceedure doesn't help, you know you've got bigger problems, most likely the clutch or your input shaft.
Good Luck!
[This message has been edited by Unit 5302 (edited 01-29-2001).]