DFrank,
I went the same route you went. Almost:
I had the factory CD/amp combo and decided to switch out the ford spkrs for some pioneers. Then I did the deck, and just recently the Sub.
Changing the deck from a ford HU to an aftermarket HU will be the most noticeable difference, but if you're going from tape to CD, and changing the spkrs, you won't be too badly off. Just consider an aftermarket HU. Besides, you can probably get some decent coin on the used Ford HU on Ebay.
Brian