best rear end for a gt 4.6

Good question. In the FRPP catalog on page 128, they have about 9 options. As usual, I'd get a slight more heavy duty one than stock. You might call their tech line (586) 468-1356 and ask them what they'd recommend. My understanding is that a new diff is about the same as a rebuild.

You also need to state what you do with your car when you ask a question like that. How many trips to the drag strip do you make. What are you priorities? What's your current and projected power level?

my dad has the detroit truetrac in his 01 saleen. he did the rear end, 31 spline axles, and 4.10 gears all at once.

I think it really depends on what you're doing with the car, street/strip.