2004 ford explorer limited, avic-d2

I used to have a 2003 Explorer XLT with the audiophile system. I'm pretty sure everything was the same as what you have in yours. The sub amp is located in the panel on the passenger side cargo area, right next to the amp. That panel does not come off, even though it looks like it does (learned that the hard way).  If you are putting in an aftermarket head unit, then you would automatically bypass the stock system because you wouldn't use the harness for the factory sub and amp. I believe the rest of the speakers are powered off the factory radio.

Just put in the new head unit, hook up the new speakers to the existing speaker wires, and then hook up your rca's to your aftermarket amplifiers and your good to go.