Don't have time to provide specifics, but that second harness is mostly speaker connections. That set up hasn't changed since 1995, so I'm not sure how it would have worked on your old X without using the second harness...

Let me know if you need more specific detail and I can provide it later today. I just installed a new Pioneer HU and it worked perfectly (what an improvement!)

I did notice one discrepency in the harness I bought and the wires on the factory harness - looked like it was ground related but since I grouned directly to metal behind the dash it did't matter.

Also - did your old or new X have RockFos? - that could make slight diff. If you ignore the second harness MAYBE you were still getting signal to your RF amp on the old one???