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Its not really that big of a problem. It just depends on whether you want to keep the factory upgraded system or not.
If you do, Then there is a harness that will take care of getting the speakers to work and getting the head unit to turn on. After that you have to take the connector that plugs into the back of the of the factory radio and splice that. You can either take a step down connector that will step down the ohms at which the factory amplified sub is at or you can leave it and get distortion from the sub (there is an obvious chose in this). The connector that you will splice will need to be probed to find the neccesary wires, ie.. ground power and speaker. Then just hook that to your existing speaker wires on the head unit and to the spliced connector. I have had to do this on my 98 explorer, eddie bauer. It had the Mach audio system.
Do like I did, yank ALLLLLL that stock, weak crap and shell out some $$$ for a real system. I put in a Pioneer head, 6x8's in all 4 corners, Pioneer 6disk changer in the console and a MTX Thunderform 10" sub in the rear panel. That should be plenty for you.
From what I have gathered.. it depends on if the speakers are 3 or 4 ohm... I have not yet taken the time to test the speakers yet, I put the project on hold for the moment. I'll get back to it when he has more money to throw at it!
As for ripping the factory out: I did a complete system in "my" truck... Alpine head, Infinity perfect corner to corner, and 2, 10" perfect subs, .. "that's enough for me!" So I know all about that!
I wouldn't mind doing this to the explorer, but it isn't mine.. and my buddy doesn't have the cash to shell out right now.