O.K., from info on the Logjam web site;
The PAC AAI-FRD3 Auxiliary Input Converter system allows the user to add up to three auxiliary input sources and have them connected directly between the factory CD changer and the factory audio systems of your 1998 - 2003 Ford manufactured vehicles with the combination of the 20-pin and 16-pin connectors on the rear of the radio (not compatible for RCU rear mounted remote receiver/amp units). I am not familiar with the "RCU rear-mounted hardware, so I cannot comment on that.
However, I can confirm that I have CD-6, and that the AAI-FRD3 is accepting R/L audio input from the DVD player. Audio input is audio input, irregardless if it is coming from DVD (2-channel), iPod, VCR, or otherwise. For me, that was the selling point of the FRD3. I added the DVD, and still have 2 more source inputs available.
You asked about "DVD-Audio enabled". I am using a 2003 factory Excursion DVD setup in my 2001. Though the 2001 and 2003 radios look alike, I am told that the 2003 incorporates the software that enables you to control and to receive audio by connecting the factory DVD directly to the CD-6. I don't recall if you are using a factory DVD player or not.
In regard to the modified harness, it was done by the guy who I bought it from. He was selling several on Ebay over time, and was probably doing it to enhance the appeal of the system. With the wiring "unharnessed", you were free to install this in a non-2003 model (as I did). And yes, it was the wiring coming out of the DVD.
The following post from yesterday provides excellent information on the wiring harness coming out of the DVD
https://www.ford-trucks.com/forums/s...0&postcount=11
Lastly, I will say it is odd that PAC would tell you that the FRD3 will not work with DVD. Were you clear with them that you only wanted to connect the R/L audio via RCA connectors? I emailed them for support, as my rear audio controls stopped working when I installed mine. I was clear on my setup, and they confirmed that there should be no impact on the rear audio controls, and that I must have a loose connector. They were right.
I wish you luck and would be interested in what you end up doing.
Les