Where oh where can I source these? Or are they not available? Seems like such a common problem (My 93 coupe has this issue) would have a common solution.
Yeah, go to the scrap/junk yard and get them. Some scrap yards might even let you have them for free. By the way, you can use the floor pan plugs out of the 87-93's and also the 94-04's. The floor pan is identical on all of these. Trust me... Ford dealer also sells them. A few bucks a piece for the big ones and about $7 - $10 bucks for a 5 pack of the smaller ones (which come in 4 different sizes and shapes btw).
I had the same problem. One of mine I noticed were missing. I noticed this when my floor was getting wet in the back sometimes. Had my interior gutted and replaced all the plugs nearly and put 2 part epoxy on them as well to keep them sealed. In the meantime while my carpet and other stuff was out, I used to drop cigarette butts out that hole at the light..hehehe