Well lets see.. no expert but I do know i thing or two.. there really is too much to cover.
1) generally rear speakers/rear fill isn't necessary. Your better off getting better front speakers
2) JL is nice stuff but you can do better for the price
3) I never personally liked the amp/box/sub all in one. Generally you can do better buying them separately.
My personal taste.. (disclaimer)
I like good sound but not going to be thumbing the neighborhood. So in my personal setup I cheap out on the amp. Which can be a problem if you running it hard or near reference levels for long periods of time especially during the summer. To me this wasn't an issue so I went cheap with amp so I had more money in other areas of the setup, like the speakers and MS-8. Also note that stock subs in Mustang doors suck so I wouldn't use them in a aftermarket setup, i use this space for tweeter. Or I get A pillar replacement for the tweeters.
I like running JBL MS-8 as converter of the signal. You need a converter anyways. (get ebay $500)
2) Speakers (comps means woofer & tweeter & crossover)
running 6.5s in the stock 8" location (6.5 speakers are most common and have best selection of component speaker for good car setup)
placing the tweeter for comps in the stock 6x8 location
Sonic Electrics has number good 6.5 comps and you can ask about the difference. I personally like a nice tweet so I like Focal's. If you are a mids or woofer fan you should go with something else.
personally like Focal something like this.. New Focal Polyglass 165 V30 6.5" 2-Way Component Speaker System FREE SHIPPING | eBay
3) AMP (again if you really going to thumbing all time get better amp) WoofersEtc.com - F100-5 - Cadence 5-Channel 1800 Watt High Power Amplifier
Then for sub get a nice 10 inch or 12 inch woofer and power it with the one amp. Generally I go with a ported 10 inch or 12 inch design. There are custom ones made for stangs if you want to pay for them.
5) Cadence has quality wiring kits for decent prices.. you go too cheap it isn't 4 gauge anymore.. WoofersEtc.com - AMPKIT4 - Cadence 4 Gauge Professional Amplifier Installation Kit CADAMP4
Now your decision will be based on your budget. If you plan to go fully active, you are going to need some sort of external processor, like the JBL MS-8 or the Audison Bit One. The JL Audio Cleansweep is a nice unit, but it is severely behind the curve in technology. Personally I'd do a single ported 10 in the trunk and run the components active by placing the 6.5s in the stock 8" location and placing the tweeter in the stock 6x8 location. If you want more umph, you could do ported 10 in the trunk, 6.5" or 8" midbass drivers in the 8" locations, 5.25" or 6.5" component woofers in the 6x8 spots, and have custom fabricated sails to house your tweeters