The pads, while they technically will fit, are not the right size for the '96 upgrade. The have a shorter height, and you basically lose the whole reason for adding larger rotors (because the pad isn't as tall as the new rotor is!).
Anyway, you may have an underlying problem with your caliper, especially is your pads aren't too old. Could be a pin that's not sliding properly, causing your caliper to remain partially closed, causing your pads to wear down prematurely, causing the rivets to eat into the rotor (gee, wonder how I know all this!). Make sure when you tear it apart you check and make sure the calipers are free to sqeeze and un-sqeeze (is that a word?).
Also, the PFCM pads from AutoZone are a pretty good deal with their lifetime warranty and all. But, they tend to dust a lot, so wax your rims really good so you can wipe them off when that dust settles on them.
Also (again), the PFCM pads do not come in the proper size for the '96 brake upgrade. If you want the correct pads, just use the stock Ford pads or spend some $$$ and buy Carbotechs (or equivalent).
Also (third time), if you buy new rotors (which it sounds like you should) I wouldn't suggest buying them at AutoZone. Used to seem like a good deal, because they came with a 2-year no-warp guarantee. They unfortunately changed their policy, and now carry just a 3-month warranty. And, at under $25 each, you know they're just POS rotors. I've warped quite a few pair (under warranty!) on my '93.
Good luck. Sorry I rambled.