Just to follow up again, I finally decided to just unbolt and remove the shifter assembly because my eyes are just not good enough anymore to discern how the harness was attached. The space was too small and cramped for my fingers to feel around.
In the end it is quite simple, so I figured I would post a pic here for any other harness-challenged people like myself!
Turns out you just push in on the front of the harness and then push/pull down on the bar in front and when the bar is fully lowered it sort of self-ejects itself from the shifter assembly. Once I got it off, it was quite evident where the problems were. I used some compressed air to blow out the connections.
Since there was still some green, I used a wire brush and cut off a few strands and twisted them together to make a mini-brush to clean inside the contacts on the harness. I did not have any contact cleaner and of course, I was too lazy to put it all back together just to be able to drive and get some. When fussing around with my make-shift brush I made the key-chime go off again, so clearly that issue stemmed from this harness. I disconnected the battery after that!
Being the impatient ******* that I am, I could not leave well-enough alone and decided to use a q-tip and rubbing alochol to try and gently clean the pins on the shifter assembly. I must have bent one and my eyes just could not see it (it was supper sunny bright out) and when I went to put the harness back in I had resistence. I saw the pin bent but in trying to get it back straight it broke off

.
Everything works without pin#8, but now instead of the D light being on permenantly, it only comes on when the lights are on and it goes off when the LR3 is off. Ironically, that is progress, but unfortunately, it looks like it will be a $250 investment in a new shifter assembly now to fix my stupid mistake in leaving the sunroof cracked.
Anyone have the wiring diagram of this harness? Now I am curious what each pin actually does.