I'm not one to post much but I'll contribute since this thread helped me out.
For the rubber window guide problem, assuming it hasn't been damaged yet, there are two things to try. 1) Lubricate with silicone lubricant. 2) If the window is not slotting into the guide properly, try adjusting the angle of the window. With the trim off, if you look at the door frame where the bottom of each rail ends, there's a black nut + washer. The bolt has a small hex slot on the head. If you loosen the nut a bit, you can adjust the bolt in and out. This adjusts the bottom of the rail in and out and, thus, the angle of the window. I'd make sure to adjust both rails at the same time and only in small increments if you don't want to risk breaking your window.
Now for the regulator, a few additional tips there as well, since that's what I was trying to repair on mine.
First, I had a hell of a time getting the push pins fasteners out on the trim. The manual shows pushing the pin heads in 1/8" will let you pull out the fasteners. I had no luck and almost damaged the trim trying to yank them out. I ended up using a screwdriver to push the pins all the way into the door and retrieved them later when I had the trim off. The fasteners are cheap enough to just replace. Part # 5GC71DX9AA.
My regulator had the same problem with the tubing separating from the plastic elbow. The back of the window was sinking and would judder when I rolled it up (cable was probably snagging at the separation point). We tried following tips from this thread to take out the regulator by rotating it within the door and ended up snapping the tube at a different spot. So we mounted it back up and picked up some polyethylene tubing (1/2" and 5/8" inner diameter) and screw clamps from the local hardware store. We cut about 1 1/2" length of the 1/2" tubing, slit it down the side, and wrapped it around the original tubing butting it up against the neck of the elbow. Then cut about 2" of the 5/8" tubing and wrapped it around the 1/2" tubing and over the neck of the elbow as far as it would go. The clamps went over the now-layered tubing, particularly around the neck of the elbow piece. Make sure the window clears the clamps when it's all the way down. The polyethylene tubing is rigid enough to act as a splint but has enough give to bend a little. It's been holding up for a few weeks now and the window rolls up very smoothly. I can even take it all the way down without issues.