So I noticed the weather-stripping that attaches to the driver side quarter window is shot... it's the piece that when vertical seals the driver side window to the quarter window. I have searched latemodelrestoration, americanmuscle, cjponyparts, etc. and I cannot locate this piece. If anybody knows where to get this piece I would appreciate it.
From what I've been able to find, that comes pre-attached to the quarter glass, so to replace it you have to replace the window. The part number (for a 99 anyway, I think it's the same on older models) in the Ford service manual is 7629710 (AR3Z-762710-A). They don't give a left/right part number in the manual, and searching the part number doesn't say which is which either. The quarter windows appear to be the same from 94-04. Got a friend who parts cars that has a set, he's going to check the drivers window seal shortly and let me know it's condition. PM me if you want his contact info (he's not into the forums, but is pretty active on many of the Facebook mustang parts groups).
Thanks for the answer! I was coming to this conclusion as well, there is a local Mustang junkyard I'm going to check out this weekend, I'll let you know if they don't have one.