The easiest way to add aux input to a Ford factory radio is with Trip Tunes.
But, I have an idea.
Recently I replaced a 6CD radio w/ steering wheel controls in a 2008 Fusion with a single cd player from a standard truck. They both had two connectors on the back of them. Long story short, installing the single disc player into the Fusion rendered the steering wheel controls inopperative. BUT, reprogramming the ACM (radio) with the correct as-built data turned on the functionality of the steering controls on the single disc radio.
My conclusion is this, that MOST Ford radios are very similar and can perform the same tasks after being programmed to the current setup. The differences are going to be how many and which connectors are on the back. Generally, the only one missing is the subwoofer if you don't have the Audiophile. Connector C290A contains all power, speakers, and such. C290C is the subwoofer. And C290B is the accessory input. Most trucks are wired for DVD and Navigation. Mine has one plugged in there with wires coming out, but i have neither of those options.
Anyway, I did some digging into wiring diagrams on the 2006 F150 (without the AUX IN) and the 2007 F150 (with the Aux IN) and found something surprising with the second 16pin connector C290B. The 2006-2007 connectors and pin locations are exactly the same, with the exception of 4 wires (pins 6,7,8,14) which of course are for the Aux in jack. Those pins are empty on the 2006 model. There is no CAN BUS lines used to control the input, like previously thought, on this setup. Haven't looked into 2004-2005 but I suspect they are similar.
The only thing that I see that needs to be done, is to buy some wiring with the connector pins attached and add an accessory jack to the already existing connector. Pretty simple if you go buy the connector pins and mount you an accessory jack to the dash somewhere. At this point it would be beneficial to check and see if the AUX button allows the use of your new AUX line. If it does not, then the next thing.. reprogramming the current radio to allow the auxiliary input. Using IDS, you can look and see if there is a programmable parameter for the AUX in, or you may have to change the as-built data. OR you could still swap in a 2007 radio. The AUX input jack doesn't have to be a ford one, just any one and you choose location.
The connector views and wiring diagrams am referring to are available below.
Before someone says "that connector has CAN BUS in it!!", those lines are going to the Navigation, DVD, or Satellite.
Anyone's input would be appreciated.