Well, guess I'll answer my own questions just to help the next guy:
If the clips come off, there are inserts along the top of the door. They're easy to miss, but there are about 9 small slits along the top. Start with the top, closest to the door lock knob. Now, skip every other slit. Once that's in you can slip the rubber seal back along the top lip of the door.
I'm not sure how it popped out, but while manuevering the rear hatch harness released. There is a very small little rubber plunger between the button and the harness. If you're not paying attention IT WILL FALL OUT UNNOTICED. I can attest to this firsthand. I got it back together and realized the button just flops around. I never saw a piece fall and figured I'd be making a trip (ended up anyway) to the parts. Fortunately, I found it a couple hours later under the car (I'd test driven a few times), on the driveway. I'll put it in when I pull the door for replacing the window switch..which leads to...
Last lesson learned. When your wife and kids are yelling for you to hurry up, don't get in a hurry with the harnesses. The harness for the side mirror adjustment WILL FIT into the window motor levers. I had the system on as I was multitasking (system check, etc) to try and get done faster. Let the smoke out and now the driver's side window switch is inop. The motor's ok because the window auto-cracks for opening/closing, and the passenger window switch still works on the driver's door.
First time I've seen a GM door with harnesses that if crossed would smoke something, then again I haven't been installing in about 15 years.
Both my rides will smoke ya
2010 L99 2SS/RS - Hertz HE HSK 165 components/PPI A404 & A600/JL Audio 10W6/Audio Control EQX, FAST Intake Manifold