I had this problem, big time here in Florida. After big rain i would have water all under the floor mat on the rear driver's side. I sealed the 3rd brake light sealed the bolts and did the drain.
Still water was coming in, soaking the floor on the bottom and up under the rear seat. So on a sunny day i put a garden hose up on roof and let it run while i was inside with everything closed up.
My water was coming from 2 places. One was from a small hole in the sealer that fills a hole right by the rear side panel (drivers side). If you take off the rear storage door behind the seat and the molding that goes to the rear door you can see the side compartment that lets excess rain flow over board. One of the rubber sealents to fill a hole rottede out and allowed water to run right into the cab.
The other area i had was the door seal was loose around the bottom of the door. with the hose running I could see water "creeping" up and over the bottom lip of the door and geeting absorbed right into the floor mat foam like a sponge.
Do this, pull off the rear door floor trim, the part that holds down your floor mat and snaps in place. If the metal clips that hold this peice down are rusty, you have a door seal leaking. Rip it out and silicone it up and reinstall.
I have been "leak-free" for a year now, but was a tricky problem for me to find where it all was coming from. I have a 2003 Trac.
Rick