I had that problem. It was from the front. In my case the mouse nest in the cowl behind the access panel under the dash rusted the metal and everything that went into that side had a chance to come into the cab. the cowl is supposed to drain down the inside of the fenders and come out over the rocker. It gets gunked up.
You can get into the wiper motor hole and there is another hole in the firewall over on the passenger side. I'd also recommend you remove the bolts holding the fender across the bottom and up the wheel well and pull it away from the truck to let the crap fall out and maybe hose it down from the cowl.
Edit- I changed the rear window seal by myself before I figured this out. PO had told me he thought it was the windshield. I eventually figured it out reading stuff on here.