First I had to put in the door brush thingies that go on each side of the window and are mounted to the door with spring clips. Getting the clips on is a bit of a chore, probably because they were the old ones and were bent a little when they were removed. A little bit of prying open and squeezing shut did the trick. They are pressed onto strips of metal at the top of the door and inside the window slot. Then the brush doodads press into the clips.
Next I lowered the window through the slot a little bit and put the window guides in the metal slots on each end of the window. I lowered the window the rest of the way to hold the guides in place. I had to put a little dab of silicone to secure them in the slots. Then I raised the window to a point where I could mount the window to the regulator using 10mm bolts. There are rubber washers and grommets, too, that protect the window from touching metal. A felt strip goes just behind the glass where it mounts to the regulator. All of the soft bits are there to protect the window from breaking and to keep it from rattling.
The process went pretty smoothly and now the doors have their windows. Another step accomplished.

The descriptions I was reading about installing the top seemed to indicate that the top fabric should consist of more than one layer of canvas. What I have is only one layer. I need to do more research to find out what to do. Just like everything else on this car, I have been learning by doing. It's a little scary. Let's hope my luck holds and I get the car done without wrecking anything!