The head unit is the "power" for the deck and door speakers. As for the 8" subs in the doors, they are powered by four amps located on the drivers side under the dash.
I have completely replaced my skipper1000 system. I highly recommend it
One suggestion is possibly consider a Scosche enclosure. They have a box for a single 12" that mounts where the 1000's sub box goes. And it fits like a glove.
If you remove the stock head unit, all you need to slap something else in there is the mounting kit for the console, and the wiring harness adaptor.
Metra 70-5521 is the brand and model number harness you will need if you intend on utilizing the factory wiring. The mounting kit is Metra 99-5807.
If you intend on using the factory sub woofer amps you will need a voltage regulator on your amp on signal wire coming from the head unit. You can get a LM7805 off the shelf at Radio Shack and it will work fine. The Ford amps expect a < +8V signal. Your aftermarket head unit is going to put out +12V. The end result is going to be a NASTY pop when the subs power up. The voltage regulator will prevent that.
As for how the speakers are going to sound with the aftermarket head unit. Only you can be the judge of that. Each person has a different ear.
Personally, I think all installing my aftermarket setup did was exploit the flaws in the factory speakers. So I replaced them also ( which I intended on doing anyway ).