Yes it will fit, everything is the same as far as mounting it up. The only other thing you will need is to swap the pinion flange with a cobra flange so it will mate up to your V6 driveshaft. Your other option is if you are considering an aluminum driveshaft from a place like Shaftmasters, let them know you are putting the 8.8 in the car and they will build the shaft for a direct fit.
You can get the cobra flange from late model restoration and others - 2003-04 Mustang Cobra Pinion Flange, M-4851-B at LRS - Free Shipping!
All are about the same price.