Bad Shaking at 1000+ rpms, any ideas?

So my 01 gt was having sometrouble shifting. It would not go into 1st or 3rdwithout jamming the shifter. After taking to my local mechanic they decided that the shift forks were worn and that they would have to pull the tranny and replace them. This was done and a new clutch was added and the flywheel was resurfaced also. after they put the car back together It began to shake at 1000 rpms. It rattles so bad that the rear view mirror will fall down. Now they can't figure out whats wrong! Right at 1000 rpms the car begins to shake and above that it still rattles a bit, but not as bad as at 1000. When you push the clutch in, and disengage it from the engine the motor still shakes,leading us to belive it is an engine problem, not a drivetrain problem. They checked the Harmonic balancer and said that that was fine, so now I dont know what to do! They are trying to tell me that the vibration could have been there before I brought it in, but i know that is BS. There was never such a huge problem until AFTER they had looked at it. I told them it had to be the fly wheel, because that is the only part that they removed that is on the engine that could cause the vibration,but they dissagree. If anyone has any ideas i would appreciate the help.

Well after a 2 month long ordeal, my car is finally fixed. It was in fact the flywheel. After posting here I felt that the flywheel was the only part that they had messed with on the engine. I told them repeatedly that the flywheel was my best guess at what was wrong, but they denied that, stating that "they were sure that they turned and replaced the flywheel to spec" After arguing with my mechanics for over 3 weeks they finally decided to take the flywheel out and check it. They found that it was turned incorrectly and was off balance. After it was re turned the car runs like a champ. They only problem now is that they broke my Tri-Ax! Luckily Steeda has that lifetime warranty and hopefully they will replace it if I send it back. Thanks to those who left imput for me!

I have no Idea exactly how they broke it, I just know that it is dfinetly broken. The preload springs are broken and it doesnt snap into 3rd like it should. Actually it doent even center anymore, just flops to one side. Im sure they will replace it, as they know that they broke it. As bad as this shop sounds they are very nice and reputable, my family has used them for over 20 years now. I just dont think they are trained enough to handle High Performance cars like a suped up stang.

If anyone has any info about the warranty on the Tri Ax please let me know as it will help me return my stang to full running condition!