Hey uh... "smelly",
I just did the exact thing as you... replaced my doors with pioneer 3-ways and put in a JVC deck.
BYPASS THE AMP!
Half of what you're paying for in the new deck is a good quality amplifier, why waste it running the sound through the el-crappo factory amp?
I got a kit which contained 3 harnesses... one for power, one to go from the new deck into the amp, and one to go from the new deck and bypass the factory amp, directly into the ford speaker harness.
I had to make a few solders (about 4 zillion, I think) to join all the cables together, but since everything is behind the glove-box and the box flips out, it's pretty easy to run your wires into the ford speaker leads.
You'll be better off... I really like the sound of those Sony units... but since I wanted mp3 and the sony is ugly, I got the JVC (which also sounds fantastic).
Any questions, let me (or the forum) know.
Brian