My DD Tracker is getting some paint and body work before winter starts.  I was washing out the inside to prep for some paint and I ran across some unexpected rust.

Inside the cab, in the rear seat footwell on the driver's side down where the floor, the footwell, and the side of the inside body meet is all rotted out.  Right at the seam and then up an inch or two.  I see there's a drain below this but mine was packed full of dirt and rotted metal bits.  I cleaned it out and can't seem to figure out what the drain is for?  How'd all the crap get in there, 12 years of random bits getting thrown in?
Passenger side is fine.

The floor and the wheel well skin in the rear are fine so since this is my beater I'm just going to fill it with roofing caulk, smooth it out, and paint over it with the rest of the floor.  Too many places on this thing with developing issues to make me want to spend good time and money fixing it right.

Does yours have the vents on the rear fender, near the tailight? Thats what the drains were for, as water can get in there and collect. I had a similar problem, didn't get too bad before I found and fixed it. The drain is in a boxed in section between the outer footwell and the rear of the outer body panel, It's also the location of the rear body mounts. That's the primary reason they rot out.  You can't see it unless you end up cutting a hole in the floor or body to clean it out which it sounds like your going to do anyway. 

No vents on the rear fender...think that's a hardtop thing like yours.

Besides...this is in FRONT of the rear wheel well.  They really have all that crap drain out there and not somewhere in the back by the tail light?

I guess that they put the drain at the low point in the bodywork, and mines in front of the rear fender well too, should be right in the area of the body mount. When I finally got around to cutting out all the rusted metal around my body mount I could see clearly into the pocket where the drain is supposed to be. The whole area was filled with mud and decomposing Nasty. I cleaned it out thourghly, washed it out, dried it out, then painted it with an undercoating type paint. Then welded in my new bodymount supports. Make the drain hole a little bigger and clean out often.