Man oh man I wish I had searched here before the past few times I've fixed my windows. I followed the writeup on understeer.com and have had to pull my door panels a few times when they pop out again. At this point I've been driving around for over six weeks without door panels in so I can cowboy repair them at will, and of course every kid on the road with a stock Mustang thinks "Because Race car".
After reading the post (and subsequent pages and pages of comments) I will be checking my tracks as they're probably the culprit. I have a new regulator arm assembly for the passenger side because it's tweaked so very badly but the drivers side was replaced a little over a year ago. I hope that I find this method to be the end all be all for this because I'd really like to throw my door panels back on and not have my mid and tweeters just duct taped to the door so i can live with a little sound (yes, because Ghetto).
Thanks for the writeup and comments, have no idea why I didn't come across this sooner! Possibly because I'm pig-headed and "know everything" as my wife suggests