I'm terrible at having the patience to document things. I just want to go and get it done. With a second set of hands, it could probably happen.
For future reference, the steps are:
1) Remove door panel. Plenty of guides out there on how to do this.
2) For door with broken glass, if you remove the speaker enclosure, you can actually get your hand and arm down in there, almost to the end. Fish out as much broken glass as possible, or it will forever be pouring out the bottom.
3) I had an entire extra door that I needed to get the glass out of. After removing its door panel, I stood it upright, hooked my door's motor control up to it, and used it to lower the window all the way down.
4) On both doors: remove the exterior B-Pillar trim by pulling the weatherstripping off, you need to pull it off to the side of the door. There will be 4 plastic pins holding it in place to remove. It should pop right up with these removed. This guide was helpful:
http://www.pexcom.com/images/Rattling-Window.pdf . Also, there are 2 stoppers at the top of the door to stop the glass from going too high, remove 10mm bolts. There is also a plastic pin near where the b-pillar trim was, I think supports the window in some cases. This needs to come out.
5) On donor door, glass should now be able to slide right out. Clean up, etc.
6) On broken glass door, remove 3x guides (not the rails), two on the inside of the door, and one on the b-pillar. Lower window motor all the way down. Remove 2x 10mm nuts holding old glass to power window rail.
7) Take glass, start by lining it up in groove made by weather stripping at side view mirror. Then work rear approximately into place. Shift and turn glass until it starts to line up with the guides. I found the guide nearest the side view mirror easiest to get to initially line up, then the one towards the rear, then the b-pillar.
8) Carefully lower glass down until it meets up with power window moving rail. Attach 2x 10mm nuts, don't overtighten.
9) Put 2x window stoppers back into place. Set to max height initially. Roll window up. Close door, adjust window, open door, etc until you get the window to a good maximum height to mate up with weather stripping on car. Move the stoppers down to match up with that position.
10) Put door trim back on.
11) High five yourself.