I own a 1999 Mustang and I decided to forego the factory head unit and get one with a CD player. This was way before the tuner module existed. I put the Empeg in the top and the Kenwood head in the bottom. It worked out great. Now I have the tuner module and can use that, or when my Empeg isn't in the car, I can use the one on my head unit. Plus I can play the occasional CD if I need to, though that only happens when friends bring their music for long trips.

In your situation, I am not sure how you're going to go about connecting the factory head to the Empeg... From what I remember the stock CD player and head unit connect via a proprietary plug. I don't remember seeing any RCA's on either the head or the CD player. It's possible they've changed things, but since 2000 was just a carryover year, I don't know how much they would have done with the radio... So you might have to find some kind of adaptor.

Just a word of warning from someone who has his stock Ford radio in a cardboard box somewhere.