Before I get into it, I've repaired and checked the trunk wiring harness (good), and today replaced the ignition switch with a new Audi part.
I bought this car a few weeks ago and knew there was a sunroof issue. One of the side rails on the roof cracked(the part the roof itself bolts to), the sunroof jammed and the PO said it was blowing fuses (naturally) so he disconnected the sunroof motor and used the allen key to pop the roof up when he wanted it open.
The sunroof motor is still unplugged. I'll deal with that issue in the spring.

Now to the fun and games:

With the ignition OFF, key OUT i've got power to all 4 windows, wipers, turn signals, HVAC blower, AC switches, cooling fans, and the 4-way flasher button is lit. With Door open, windows still work. If I push the AC/Recirc buttons they light up, AC engages and the cooling fans come on. With the key OUT.

When I remove the 363 Relay, everything loses power with the Key OUT. I switched out the 363 Relay with another one, power remains cut to everything (with key out) until I switch the key ON. Then, when I turn the Key OFF, power remains going to the above items.
Now here's the kicker: With the 363 relay OUT, car running, everything works INCLUDING the windows-- with the exception of the driver window. The situation is the same regardless of which 363 relay I use. With 363 OUT, motor turned off, the three window switches remain lit and these windows work until I open the door--which is normal.
Poking around the relay area under the steering wheel, nothing appears to be messed with.
These cars are alleged to have retained accessory power, which I think is supposed to be disengaged when you open the door. Is this a possible issue here?
The interior lights work as they should. I've pulled the door switches for the interior lights and they work, wiring good. The warning chime works and turns off when I manually push in the switch with driver door open.
The other issue that comes to mind is the plate under the battery area, where all the wiring is. This is where the cooling fans pick up power. Could someone have bolted a wire to the wrong post here causing this?
I've checked all the fuses in the fusebox and they are all good, no evidence of any melting, strange wiring issues, etc. It crossed my mind that perhaps 363 blew sometime in the past and someone mickey moused something, but I see no evidence of that.

All the dash idiot lights work as they should. It appears that with the exception of the driver window, this thing is normal with the 363 relay out. Bizarre to say the least.

Any thoughts?

 

I think that the original ignition switch was connected incorrectly. By replacing the switch, you upgraded the condition of the part, but by wiring it the way you found it, you did nothing to improve upon the "dumb-assery" of whoever wired it wrong to begin with.

I recommend checking an official wiring diagram. If there's a red wire (or whatever the "always hot" wire color is) and a blue wire (or whatever the "ignition hot" wire is), I think they're swapped.

HOWEVER: I am absolutely NOT an electrical expert. I'm only throwing the first and most logical idea that comes to mind.

 

Are you 100% sure you have the correct ignition switch?

When I bought a replacement from a Euro parts store the guy grabbed a switch that was identical looking to my original switch. When the price was a lot hight than originally quoted he looked it up again in his computer and said it was the wrong switch. He went and grabbed the correct one and it worked great.

 

>Before I get into it, I've repaired and checked the trunk wiring harness (good), and today replaced the ignition >switch with a new Audi part

Well, every body said yes. You are mistaking on wiring connection back of ignition switch! ! Check over again.

 

My recollection is, the plug going into the switch only goes in one way. I believe there were at least two alignment pins on the back of the ignition switch, leading me to think it only plugs in one way.
But, as this is wild problem, I'm going to check that out again, as I am of the opinion that every idea is a good idea. I really hope this will do it!!!