I posted this in 4.6 too, but I figured anyone could help with this problem, as my car is basically a foxbody from the trans back :

Well the shop called yesterday, and I went to pick up my car today. Stupid shop is 2+ hours away

Anyways, I left and was running about 40 MPH for awile with the windows down to listen for noise, and I didn't hear anything. Then, we got on the highway and I rolled up the windows. The freaking air didnt work!!! The shop was already closed, so I said f it and went to get something to eat. After Hooters I got back on the highway and suddenly the air conditioner works. It kept working all the way home, is ice cold as usual.

That all sounds like good news, except that once I got the windows rolled up and the air on, I noticed a vibration. It is noticable at about 65-70 MPH, and at 75 it feels like a car when the rotors are warped and you mash on the brakes.

I am suspecting that something is wrong with the U joints/driveshaft??? The noise seems to be coming from the rear of the car. What else could be wrong? It keeps getting worse and worse the faster you go (only took it to 85 or so, supposed to be easy on the new clutch for 500 miles) so I don't think it is a misbalanced tire???

Any info here??? Also, the trans makes more "gear" noise than the old 45. Is this normal in a TKO series trans???

 

Sounds to me like your drive shaft is not seated right, possibly one of the u joint caps isn't all the way in??You could get more gear noise from the TKO than a stock one but wouldn't worry about that.It could also be the shifter do you have an aftermarket one cause they will make more noise??My friend got a new TKO and it has a horrible vibration in it and its was new also.Something could be up with the tranny also .It sucks your that far away from the shop because you could have to make a couple of trips there to figure out the problem.If you pull the car out of gear while your driving and coast does it still vibrate??If it does chances are its not the tranny its the drive shaft.As far as the Ac not working ...they should have touched anything to mess that up it might just be a coincidence that it stopped working after the tranny went in.Next time it stops working see if the clutch on the AC compressor is engaged or not that will limited your problem down to were it might be

 

The vibration contiues when the car is in nuetral or the clutch is pushed in. I am starting to lean towards the driveshaft. I got it up on a lift for 20 bucks and had the guy rotate the tires while I watched it. I can acutally see the driveshaft slightly moving up and down!! I assume this is causing the problem??