I have forgotten what the rubber looked like before the car was painted. This piece with two sides and a long middle appears to belong to the top of the window, but when I put it along the top of the window the sides don't seem to work at all. The rubber has a slit made to slide over the top of a seam, but the seams on the side and the seam on the top are not in the same plane. What am i doing wrong?

The rubber sides of the seal attach to the chrome trim pieces. With the chrome trim in place, the seal will align.

There is a tab on top of the trim that goes inside the corner of the seal and is supposed to be held in place by a tiny setscrew.

That piece gets put into the trim piece that is screwed into the window frame first. Hard to do. Use soap and water.

this is the trim piece you need

The chrome holds the seal you'll be fine once it's in.
You will notice the chrome piece is slotted. It's so you can adjust the spacing.