Lets take time back 6 months. My throwout bearing was going out in my 2000 3.8L manual. I order a new clutch kit and have it installed at a local dealership.

Enter 1 month ago, the clutch is still giving me lots of noise and my whole transmission is vibrating at 70mph or more. I have a tech look at the clutch, ITS SHOT! The flywheel was bad 6 months ago and was never replaced. This caused deep grooves in the new clutch. I order a new clutch plate and flywheel (externally balanced)from Autozone. Tech installed it, motor now has the shakes.

I order and wait for a flywheel directly from Ford. They even ran my VIN. Flywheel arrives, installed, wait....this is an interally balanced flywheel you ordered. Turns out for don't make externally balanced flywheels for my car. Oh....and local auto stores can't even order one. So I find one online. Externally balanced...installed...and STILL has the shakes.

I have already installed a new harmonic balancer, the car is not misfiring, only the motor, bell housing, and starter are hooked up.

I have been with out my car for 3 weeks waiting on different parts. I NEED HELP! AND FAST!!

 

Just a guess but you might have a bad u joint on the driveshaft. That would make tranny and car shake at certain speed.

 

Out of curiositiy, was your car making a fairly loud noise when you were in 4th gear? It would get louder as you accelerate and dissappear if you press the clutch or release the gas? It also makes a skipping noise if you lightly press the gas. This sounds like the same problem I'm having currently, and I'm trying to figure out where exactly the problem lies so I can take care of it.