Gears Stick When Engaging???

If you can do the work yourself, or know someone who will do the work for you, then you dont have to worry about the cost of "labor fees". However, if you can't do the work yourself, expect to pay about a full grand or so for a professional to drop the transmission out, rebuild it, and then re-install it.

Personally, I'de just buy a new transmission instead of rebuilding it.

Find another Mustang...there are plenty out there. I know this is hard to do when you fall in love and get your heart all set for this one car, but look into the future a bit. Sounds like a major bill and lengthy time in the shop. Even then it may never be the same as it once was. And this may be just the proverbial tip of the iceberg.
Do yourself a favor and find another 5 spd GT and don't compromise. You'll be happier in the long run. You'll look back at the trannie challenged GT and be saying, "Thank God I didn't buy that one."