Like many FSJ owners, I had tailgate window issues. It would make a lovely popping/grinding noise whenever I put the window up. In order to get it into position, I consistently had to grab the top of the window and pull it up at least halfway while engaging the key in the tailgate. Not fun, of course. I started by dropping the window and the tailgate. I ordered a tailgate channel from BJ's last week so that when I dove in, I'd have the materials I needed.
The first step is to drop the tailgate and remove the carpet and the access panel. Just take out the fourteen screws holding the chrome metal strips in place on the carpet, and then take off the twelve that hold the access panel. Stay organized, however, because these screws are at specific lengths to avoid hitting anything of the internal workings of the tailgate itself. Here's what I found.

In the pic below, notice the two large gears with the 1 1/4" flatstock steel bars. As the motor rotates the driver's side gear, it moves the flat bars which are attached to the lifter channel via small bolts and a pair of spring-loaded washers.







I added little green grease, and now I'm done. After buttoning the tailgate back up, I had a fully compliant tailgate window. I think when I'm bored and in the mood for some quick little project, I'll open the tailgate back up and glue the plywood strips together and use some silicon adhesive to hold the plywood to the tailgate wall.