After a ton of research, i finally got my sony radio installed and working properly with the stock amps, subs, and tweeters. I though i would make a post to eliminate the confusion for anyone else that would like to convert theirs so it's a little easier for them. Hope this helps...
First thing, here's what you'll need:
Adapter harness, this one is the only one that will work... trust me, i've discovered this throug trial and error
Ford Receiver Wire Harness For select 2001-03 Ford Mustang and 2003 Lincoln LS models at Crutchfield.com
As you can see, it only has two plugs YOU DO NOT NEED THE THIRD ONE! However, the small plug is important, as it is completely responsible for controlling the amps. If you make the same mistake as i did, and do not get the correct plug, you'll end up listening to your tweeters. The amps need a low level signal coming from the radio, and therefore require an RCA connection. Also make sure you wire up BOTH amp powers (blue with white stripe) and BOTH amp grounds.
THIS CONTROLS BOTH FRONT (in door) AND REAR SUBS
The remaining tweeters are controlled by a high level output, and can be wired straight into the harness for your after market radio.
You will also need an adapter plate to adapt the stock opening to a normal radio size. ( the one i got wasn't all that great and required some fabrication, i would recommend trying the one from crutchfield)
LASTLY AND IMPORTANT!!!
Make sure you either buy an aftermarket radio that can limit High frequencies for the bass, and low levels for the tweeters, or you will be pumping bass out of your tweeters. You can also do this by wiring "Bass Blockers" into your harness. The stereo i ordered was able to control all of this and did not require bass blockers, i highly recommend it, but i'm sure there's other one's that have the same function
here's the link for the radio i purchased, it's nice because you can change the light color to green to match your gauges and it has usb capabilities that work great for playing music off my blackberry
Sony CDX-GT730UI (cdxgt730ui) In-Dash CD Receivers with MP3 / WMA Playback In-Dash Car Stereo Receivers and Head Units Car Audio and Video - Sonic Electronix
Well i think that's about it, i'm sorry for the lengthy post... just hoping this will keep people from going through the frustration i had to
If anyone has any questions, just ask
02 GT --> long tube headers w/ x pipe and flow masters, throttle body w/ intake plenum, cold air intake, short throw, 255 nitto 555's all around, 373 diff gears, 2 inch lowering kit w/caster camber plates, sony radio working with stock system