Both the GT & Cobra's are 50 oz balance. They are interchangable. The only difference is the Cobra total weight is a little less than the GT's, only 3 lbs lighter in total weight, not the balance weight.
The one you got from Summit will work, even if it is for a fox. I have a fox billet...
Just my opinion, go ahead and do it. If you weld around the hold after you drill it, it should not weaken it too much. It would be better and stronger than not doing it.
As stated, no forge internals. Hyperutectic pistons. Same crank, rods & block as all other 5.0 Mustangs from like 87. With a good tune (keep detonation from happening) and low boost, below 10 psi the motor "should" last for a while.
The E cam is susposed to be good with the 94\95 computers & has good mid range power, but falls a little short on the upper end, good tq.. Stay away from the B cam. Not sure on the F?