This posting is going to be a real lazy post for me. Since I already wrote the installation instuctions for CJ Pony Part's site, I'll link to those instructions. Besides, they're better than the documentation I normally do here anyways...because I'm lazy at this stuff.
One note...I used Ford tooling weatherstripping for both (also shown in the links) and highly, highly recommend this route. Generally Ford tooling parts come at such premium and most of us just can't justify the cost. But for something small like this, where you might be looking at $30 compared to $15 for an import, it's still doable. For such a small premium, the window seals play an extremely important roll--exact fit ensures no leaks or whistles. And they're made in the USA.
Vent window seal installation
Quarter window seal installation