I have never put gears in, but I do know that it is very labor intensive and very exact. If you don't do it right, you can ruin them pretty fast. If you have never done it before, then I would suggest that you have a trained person to it instead. Take it the a gear shop, and be sure that they have done a Ford 8.8 before.
Many gear shops that cater to the Mustang crowd will be able to help you out.