After a month of real life and no free time, progress!
The first thing that happened is the junkyard misfiled my order as "local pickup". When I didn't hear anything after 2 weeks, I called them up, and they were super apologetic and charged me $50 for 2-day shipping instead of the originally quoted $102 for ground, so that's ultimately a win.
I immediately turned around and spent the money I saved on these absurdly overpriced things. These are L-shaped blades for an oscillating saw that you use to cut through old urethane. I originally bought them to remove the blank panel in my van's door non-destructively, in case something went wrong with the window and I had to put it back. I don't know if there have always been different sizes of oscillating saw chuck, or if there's a standard for most applications, and a separate standard for the special tool a glass-shop uses, but these blades don't actually fit my saw. The panel is pressed in so tightly that cutting it out was a huge pain, because the saw would vibrate its lock-bolt loose and the blade would try to rotate, so I had to stop and readjust a bunch of times. You're also not going to be able to cut into the corners, so once I had cut around all the straight edges, I basically just kicked the shit out of the panel until it popped out.
Then I unbolted the door from the van, which is 2x T40 torx on each of the 3 hinges. The top bolt on the middle hinge (I've marked the hole) is tight against the hinge and you can't get a ratchet on it, so I used a 3/16" allen key. I also dropped this foam-shaped oval seal on the ground; it covers the electrical contacts on the door. I was ultimately left with this:
Next I cleaned all the old urethane off the pinch weld. I started with a normal razor blade, but this ended up being pointless. It was too hard to get into the corners, and it turns out the oscillating sawblade absolutely obliterates old urethane on an open surface. Knowing this, I wouldn't do the job without it, even if I didn't care about saving the fiberglass panel. Once most of the urethane was gone, I cleaned up the remainder (and a bit of rust here and there) with a flap disc, then masked and hit it with white spraypaint.
While the paint dried over the next few hours, I started prepping the junkyard window. They sent it to me with what looks like 100% of the urethane still attached to it, complete with taxicab-yellow paint. I tested really jamming the oscillating sawblade against a random piece of glass I had lying around; it didn't crack and barely scratched at all. So, I felt comfortable using the blade to clean up the junkyard window. After a couple passes, I cleaned everything up with rubbing alcohol. I found a 3M windshield replacement instructional document that said to remove old urethane to 1-2mm max, and I definitely got below that.
Because I was dealing with old urethane, I decided to use primer this time around, which I didn't do on the back doors. It turns out that glass urethane primer is stupid expensive--like several times more expensive than the sealant. The 3M stuff is available in two sizes: enough for a handful of windows, and enough for all the windows, ever--but more importantly, it goes bad in a week after you open it. I decided the most cost-effective solution was this thing, the Betaprime single-use stick. You screw the tip all the way on, and it breaks the seal, then you apply the primer with the foam applicator. It's pretty much guaranteed to fall apart by the end of the job, and from what I've read, the primer is even nastier on skin than the urethane. I primed both the window and the pinch-weld. The 3M document says to let the primer dry for 5-10 minutes.
Finally, I applied urethane from the second tube I bought during the first half of the project, again using the V-notch method. I also ran a second bead diagonally through each of the corners.
Six hours to set up, and the door can go back on the van. Still need to clean the outside of the window glass, as well as the window's sliding track, because the window as it arrived won't close quite far enough to latch. May also redo the bumper stops, which are just sheet metal screws right now. I feel like there should be something softer in there to protect the edge of the glass.
I'll also post up some measurements of the glass-in-glass window, in case somebody in the future who really, really wants one ever decides to have one custom-cut. I will note that the visible area of the window is limited strictly to the slider, which I didn't realize before. The fixed-glass windows have narrower black bezels on all sides except maybe the front, and so will offer better visibility.
Final cost for this part of the project: $90 (window) + $50 (shipping) +$48.70 (sawblades) + $11.67 (primer) + miscellaneous shop supplies. Total cost ~=$201.