Well,
I took everyone's advice and found a new mechanic/place to get my gears done.
Although the mechanic that did the job in the first place is friendly and has proved to be a good general mechanic his experience with gears was mediocre at best (unless he sold me a set of shoddy gears).
I bought a new set of Ford racing gears (3:73) and had a garage do the work. The car runs smooth with no sound from the rear at all!
That being said I was "taken for a ride" when the previous mechanic sold me a used set for 200$ on behalf of someone else (another customer of his). Turns out brand spanking new gears for my car are $215 + tax straight from Ford (I guess I'll do more homework next time up front and not trust what people say so much).
Lessons learned I guess...so I will now enjoy my gears which have now set me back approx. 1700$ (including previous mechanics work as well as new garage and 3 sets of gears). An expensive lesson but it will never happen again.
Thanks everyone, Marc (88 Convertible GT 5.0)