You're in better shape than some since you have the antenna connector behind the head unit. That means your head unit IS actually a tuner and not a totally dumb controller. It controls the amp power and sends the preamp signal to the amp in the rear. (I'll try to upload some schematics later so you can see the details)
There were at least 2 or 3 possible system configurations, some where the head unit didn't even have a tuner built in. I know on those the amp was interfaced to the head unit with a proprietary control bus. However, your system is different as the tuner is built into the head unit, and I don't know what the interface is between the head unit and the amp. If it's a simple trigger signal, then it may be possible to interface an aftermarket radio to the stock amp.
The conventional way to do modify the system is to get one of those adapter harnesses to extend the speaker wires from the back quarter up to the dash, and then connect those wires to the speaker output on the aftermarket radio (or in your case the newer Ford radio). Like I said, I'll post some schematics later so you can see exactly what's going on.