The engine vibration you are having is more than likely a bad harmonic balancer. Not at all uncommon on the 94-95 cars with high mileage.
While it is possible, I doubt it is due to the clutch install; it is pretty tough to screw that up that badly and still have everything go back together at all. Unless you damaged something pretty bad.
btw, a better option than the rear wheel spacers, is to convert to an 03/04 IRS
That's what I did w/ my 94 Cobra.
