Ok, for those who have read my post about the factory HID headlights above and why there seems to be two different wiring harnesses (one for halogen and the other for HID) I am pretty sure that I have the solution. I found that the HID headlights (which includes the entire headlight assembly) would interchange with the halogen one physically, but there were minor differences. First, the plug for the HID is slightly different, but it can be forced.
I went ahead and purchased not only the 2004 Aviator shop manual, but also bought the 2004 Aviator electrical manual. It was there that I found out the difference and I have a theory on why Lincoln decided to do it that way. First, the differences. The most important difference is that the fuse box, located under the hood, uses 10 amp fuses for the halogen headlights (I believe spaces 33 and 34). These are small micro fuses. The HID headlights use the larger 20 amp fuses, which are in empty spaces on the halogen fuse box. Also, the wiring to the HID relays on the passenger fender well from the fuse box is 16 gauge compared to the 18 gauge for the halogen lights. All wires are the same color, however. Also, from the HID relays to the actual HID plugs, again we find 16 gauge wires, instead of the 18 gauge halogen wires. Again, the wires are the same color, just thicker. So, my theory is that the HID wires must pull a larger amperage and trying to pull that amperage through 18 gauge wire would probably cause the wires to get hot and overheat and possibly start a fire.
What I find strange is that I have also upgraded a 2004 Lincoln LS from halogen to factory HID, but that was strictly plug and play and I drove that car a lot at night and never had any issues. I do not know if the halogen wiring harness was just thicker on that car, allowing for the HIDs to just be plugged in, or if I was just lucky. Too bad the ex got that car in the divorce, or I would check to see the wire diameter in that car.
Finally, I did manage to incorporate the HID wiring harness into my Aviator. The hardest part was working on getting the blades from the HID 16 gauge wires (lt. green with white stripe and a solid white wire) to go into the fuse box. Once I got that completed, put in the 20 amp fuses (pulled the 10 amp fuses from the halogen setup) and put in the battery, I found that the headlights are always on, somehow completely bypassing the light switch inside on the dash. My thoughts are that the blades that are found in the HID fuse position in the halogen fuse box are attached to a bus that is hot all the time. So, Saturday, I will go out to the junked Aviator and look at how the power is given to the HID fuses on that vehicle and see if there is a difference.
Anyway, after working on this vehicle now for a few weeks, I am finding that it is pretty easy to work on. If you have worked on other Fords/Lincoln/Mercurys from the 90s through the mid-2000s, they are pretty straight forward. Invest in the factory mechanics manual and take your time and plenty of pictures of how things are before messing with them.