6x8s in the doors and the rear deck with 8" subwoofers in lower part of the doors. The front doors have a Mach plate that consists of a tweeter and a mid component that fits in that 6x8" hole.
I replaced my door and deck speakers with some Infinity Kappa 682.7 CF 6x8s. Everyone I spoke with said they would not fit, and the only thing required was to bend one of the screw hole tabs up and find a place to mount the crossover. It took me all of 2 minutes to do that! NOW, if you want to run your own wires to the doors instead of using the existing wires, I wish you lots of luck because the existing door harness is a royal pain to try to squeeze wires through.
To complete Phase 1 of my system upgrade, I also replaced my Skipper 500 deck with an Alpine CDA-9885. If you wish to retain the factory amps and 8" subwoofers, I highly recommend getting a 5V voltage regulator from Radio Shack (Model #7805, Catalog number 276-1770) to eliminate the turn on thump. If you are replacing the door subs and adding another amp, disregard that comment.
Now I am on phase 2 of my upgrade. I purchased a Rockford Fosgate Power 1000 25 to Life amp and I am about to order a 12" Kicker solobaric subwoofer to put in the trunk. When all is said and done, I will have a true "Shaker 1000" system for less than what that costs as a factory option. I am also going to set my subwoofer up so that it can be removed, if need be (i.e. to change a flat, go on a trip, run down the track, etc.).
Maybe I will buy a 2016 Mustang GT, maybe not...