If they replaced your GT rearend with a V6 rearend then you got royally.....use your imagination.
One of the major differences between the V8 and V6 platforms is that the V6 uses the wimpy 7.5" rear axle. The GT uses the much better 8.8". They throw that stupid 7.5 in there because salvage units are extremely easy to come by. Then you wonder why the first thing that happens when you put any decent torque to it is the destruction of the rearend.
Check the housing and see which you have. If they did indeed replace your 8.8 with a 7.5, that punch in the head is not only well deserved, but pretty much mandatory.
Even if it is an 8.8, they didn't check for leaks and probably didn't check the fluid level either which is just plain negligent. That squealing means your internals were getting ground up. Don't put up with that. In any case, at this point, a newly remanufactured unit in not unreasonable. If you don't get satisfaction, call an attourney.
Also, I don't think that squeal is the E-brake, I think it is improperly set gear backlash. Each housing, differential, and gear set, need a shim set matched to them for proper backlash tolerance. To tight and it whines, to loose and it gets clunky grinding. If any of those components came from a different unit, they have to reset backlash using new shims, which takes a lot of time and gets fudged A LOT. Ask if they set the backlash properly, I think factory spec is between .004" and .012". They should have written down what they set it to. Don't tell them what the spec is, just check their knowledge. If they didn't set it properly, LIGHT THEM UP!
Sorry for the rant, I have family that specializes in this field (I used to myself). If we had ever pulled the stunts that those people pulled they would lose their contract with the insurance company to say the least, and we would have been sued for sure.