Here are the parts for my system:
Front Speakers:
Infinity Reference 6832cf (component speakers)
Rear Speakers:
Infinity Reference 6832cf (2-way speakers)
3rd Row Speakers:
Infinity Reference 1031t (1" tweeters)
8" Subwoofer:
Polk Audio db840
Amplifiers:
Kicker 08ZX200.4 (35w x 4; 2 of them) - This model has been discontinued now though, but you can probably still find them on eBay or something similar
The front and rear door speakers were direct replacements (size 5x7/6x8). For the tweeters in the front doors, which are part of the component system, I had to enlarge the stock openings a bit with a Dremel tool, but then they fit like a glove. For the 3rd row tweeters I just used a hole drill bit to drill the hole. I mounted the two amplifiers under the second row captain chairs. Even though the sub is an 8" sub, Ford uses a speaker that has mounting holes that are actually closer to 9" so I made an adapter out of a piece of MDF in order to install the new sub in the factory sub box.
One amp powered the front and rear speakers. The other amp powered the sub and 3rd row speakers. I also ran new, quality, speaker wire between the speakers and amplifiers so that noise would not be an issue. Everything sounds so much crisper, clearer and louder (although I don't really play my music loud). The bass is much better as well even though it is still an 8" subwoofer. The bass will not be heard 10 blocks down the street, but I wasn't looking for that anyway. I have been so impressed with the improved sound quality over the OEM system (and I thought the OEM system sounded pretty good) that I am considering getting satellite radio for better, clearer content since my upgraded system really amplifies the "flaws" in standard and even HD radio.
Below are a few pics...