I got some terrible shaking in my mustang

Ok first off, I haven't been on these forums in three years. I only come on here as a last resort. I have searched for hours and can't find an answer to my problem, so I'm gonna ask the pros. I have a 2000 mustang v-6 and my TOB went out, so I replaced the whole clutch and had to buy a new flywheel, because they said it wouldn't do any good by turning them. Well I didn't have the tool to remove the pilot bushing, so I had to bang it out. I mean I really beat the crap out of it to get it out and finally got it off. Then I replaced everything, took 2 days, but finally got everything together. I went for a test drive and when I turned on the car it shook kinda hard. I thought that after I drive it for a while it would fix itself, but thats not the case. Well to some it all up, the car shakes pretty bad, while just sitting there in neutral it shakes, when in 1st gear it shakes, 2nd gear shakes, 3rd gear shakes. I try and gun it and it sounds terrible and shakes like crazy. I can't think of anything except maybe when I was banging the pivot bushing (not sure the name of it) out, maybe I messed up the harmonic balancer, or maybe the flywheel is defective. I can't think of anything else. Please help me...... One other thing I was thinking about, was maybe it was some sort of vacuum line got disconnected, but I couldn't see any disconnected. Throw any ideas, even if you think it might be dumb, shoot them my way please.

Please don't get upset about my screen name, I made this account when I was upset and I was having problems with my car.

any other ideas? someone said i might have bent the crank when I was banging the pilot bushing. another tip I got was to remove the harmonic ballancer and run the car to see if its still shaking. if it still shake, then its not the harmonic ballancer. the other thing is it might be a defective flywheel or the burrs. another thing is it might be a vacuum leak, or motor mounts.

yes there were burs, and we removed them, and reinstalled the flywheel and put everything back together and it still shakes.

HELP!!!

ok, I have an update. I removed the flywheel for the 4th time and took it to o'rilies auto parts store and had them put the flywheel on the resurfacing machine just to see if it was ok, but it was bad. It wobbled on the machine. So I went and exchanged the flywheel. I took the new one back to Orileys and they put it back on the machine and it was good and straight. So we went and exchanged the new clutch for a newer clutch and put everything back together. I started the car and thought everything was perfect. Then I reved it to about 1200 rpms and it started to shake a bit. I reved it higher than 1200 and the shaking went away. It only shakes now at 1200 rpm. Its funny. Now Im really at my wits end. Any other ideas???? What could cause the car to shake at 1200rpms only? I mean the car shakes very little at all other rpms, but thats just car shake, nothing that stands out. BUt the 1200 rpm mark is where it is very apparent shaking. I don't remember the car shaking before this project started.

I was told the motor mounts were real good. But could the motor mounts go out from changing out a flywheel, because it didnt shake at all before we started the project (replacing the clutch). I havent put more than 10 miles since we replaced the clutch, because of the shaking. I don't want to further mess things up by driving it. The car starts right up and it doesn't seem to be anything wrong with the ignition.

Update, I have a factory new flywheel, and clutch. Still shakes at around 1500-1800 rpms.

I did not support the motor while the trans was out. And the motor mounts have never been replaced.