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Left window stuck in open position. Following the 'do the simplest fix first' protocol, I replaced the master switch assembly. No luck, so I ordered a new motor. Since I was going to have the door apart, I also ordered the upgraded the R35 GTR door stoppers. I replaced the right (passenger) stopper first. Then, for some reason, I tried the driver's window switch - the window worked. Not wanting to mess with fate, I breathed a sigh of relief and moved on to the door stopper. When I removed the speaker, I found this:
I think it must have come displaced and jammed the window in the open position for a while before coming loose. It looks like it fits into the front channel of the regulator, cuz there's a little tab at the top of the regulator channel that matches up with the hole in the rubber. Am I on the right track? If so, are there any tips for getting it back into position without removing the whole panel?
You're 100% on the right track (no pun intended). That piece slots into the window track channel (towards front of door). I was having the same problem with this piece falling down into the bottom of the door skin. I used some very thin double-sided trim tape to make it stay in place. After re-installing it (hopefully for the last time), I recommend putting a long lasting rubber conditioner on it. That will help ensure the window travels cleanly and smoothly in the track without attracting dirt/dust and causing it to gum up. A silicone spray also works wonders for conditioning rubbers, but if you get it on a surface you ever want to use double sided tape on or need to re-paint, etc....it's a real nightmare to remove. In short, use silicone products with caution around vehicles.
Your best bet is to remove the window glass and pull out the regulator assembly. It's more work, but worth the effort as this gives you a chance to clean/lubricate the regulator and also re-adjust the window glass if it's not getting a solid seal against the door frame weatherstripping or it's not cracking open properly whenever you open the door. That being said, you might be able to re-install this piece through the speaker hole, so long as the window is all the way up. Give that a try 1st.
Last, regarding your intermittent window switch issue. You could have a damaged wiring harness at the door hinge grommet (the part that flexes/bends as you open and close the door). You can do some experimentation/tests by opening the door at various angles or wiggling/tugging the wire harness at the joint while operating the switch. If you can re-create the dead window motor scenario, then that would be proof of a bad wire in the harness bundle.