Its not the tranny that you need to worry about, its the rear end. The GTs come with an 8.8 inch rear end and the V6s come with a 7.5 inch rear end. If you drop in a V8 and start driving your car hard on a 7.5 inch rear, things start to break.
You can always find stories where guys have done the swap and the 7.5 has held up fine, but the fact is, if the 7.5 was fine then Ford wouldn't make the 8.8.