Well, this was a fun little journey. Thanks for the pics, doug7740. I was able to contrast and compare with what was under her 'Bird's dash.
Found those two extra wires that were tapped into the main harness, followed them up to where they ended, and found a chunk of a unit there that was zip-tied to the main harness. It had all kinds of numbers and stuff on it(none of which were Ford
part numbers) so I did some internet sleuthing and found that it was/is a LoJack system module. Definitely dealer installed, though. If this is affecting the power supplied to the window master switch circuit, I would assume simply unplugging it would remedy it. However, the wire it appears to be tapped into doesn't appear to be either the YEL/RED, or RED, or any of the 12V source wires involved in any of the
wiring diagrams you provided earlier. In fact, it looks like it's tapped into a GRN/GRY wire. I've attached pics of what I found, including the wiring loom that was empty and left under the carpet. Weird.
I did, however, check any and all connectors in that area to make sure they were all firmly connected and all their wires were properly seated. I checked every connector attached to the
FEM, every connector that went to/through the firewall, and every connector that was attached to that little block that hangs just behind the hood latch release lever. No change to the operation of the windows.
So, the situation remains the same: Both windows auto up/down sealing feature still works reliably. The 12V source power out from REM is good. No power to the driver's master window switch. Jumpered power from REM to master switch makes both windows work, from both switches. So, for some reason, that 12V power from the YEL/RED isn't making it to the master window switch. No DTCs present.
What am I missing? It seems like the solution should be fairly straightforward, but it eludes me, and apparently others here.