Getting the side windows back in when it's cold out takes a special kind of masochism, to be sure. Luckily, it gets easier the more you do it. Having a good top helps a whole bunch as well. The dealership put a Rampage top on mine to replace the worn out factory unit. It fits OK, but not exactly right. The little details on it suck, and the zippers are pretty cheap. It works, but another Rampage is NOT going back on when this one wears out. Hopefully that happens soon.
Here's how i put the side windows in: Start the zipper about three or four teeth. Put the front flashing into the door surround and make sure it is well and truly seated. Hook a small chunk of the Velcro on the rear, upper side of the window. Finish zipping the window in. Hook the lower flashing into the body channel. Tug the window flat while attaching the rest of the Velcro starting at the top and working back and down. Seems to work OK, even in the cold.