transmission vibrating

just in stalled new fly wheel on my 86 foxbody mustang and know the transmissions vibreating

Check your transmission mounts.

Also, I think it's possible to re-install the drive shaft 180* out of position from its original configuration. (Just going from memory here).

If so, that can cause an imbalance and a vibration.

Try unbolting the rear driveshaft universal joint and rotating to a new position and re-installing.

You can also improve driveshaft balance by tightening a hose clamp around the driveshaft, and then moving it around until you see improvement.

If it's not mounts or driveshaft imbalance, I'd pull the tranny and take a look at the flywheel installation again.

Good luck and let us know what turns out.