Just thought I'd chime in here. I have a 2006 Pony, and since it didn't come with an audio-in jack, I bought a third party adapter that plugged into the back of the factory deck. Since the factory decks have an AUX setting, this little box just converted an RCA input (Red/White left and right connectors) to the CANBUS connector on the back of the factory deck. If you search google for IPOD and Ford Mustang you'll find the unit. It's about the size of a pack of cigarettes and costs around $100. Super clean sound out of it, and you just connect your iPod to it using a 1/4" to RCA audio cable that you can get at Radio Shack for $5. Then just select the AUX setting on your factory deck and you're good to go. Use it with a Griffin RF remote for your iPod. You can just leave the iPod in your center console glove compartment and use the remote to shuffle between songs.
Now, if you want to connect the iPod to a deck and have the deck display song titles and have the iPod controllable through the faceplate I recommend buying a Clarion deck with CeNET interface, then purchase the necessary CeNET cable that connects directly to your iPod's data port. That's how I have my '
Stang set up right now (the factory deck and philco speakers are ass for fidelity).
If you need any advice on connecting your iPod, throw me a private message and I'll send you some photos and schematic instructions. My baby is set up so that not only can I connect my iPod, but I also have an additional AUX jack for my PSP or portable DVD player. The Mustang makes a great multimedia center!