Mine was doing this last spring (I had removed the carpet becuase of it, and one day I opened the door, and water actually poured out... There was that much in there), and I ended up taking the driver's side fender off one day (to remove a dent) and found a pin sized hole at the bottom of what looks like a molded metal box, under the cowl drain. I hope that made sense... But anyway, I took a very small screw driver, and poked it up in there, and wiggled it around, etc, then I also tried a paper clip. I would wiggle it around, then pour water into the cowl from a hose. After that, stick the screw driver back in a keep jaring the stuff loose, untill you think it is unplugged.
That's what I did to mine, and I have not had a leak since I did that, and it has rained pretty damn hard a couple times.
Also, when I first got the truck, I had taken the drivers side fender off (truck was wrecked) and when I was cleaning the truck, I noticed a couple leaves stuck in the cowl drain. It was deffentally more than a couple, I'd say a hand full or two. So, that could be your problem as well.
As kind of a test, you could lift the carpet back and dry the floor around the front left corner, and then just take a hose and hold it on/ in the cowl, and see if after a few minutes you see water seeping through onto the floor. Could also try the same thing with the windshield seal, except holding it on the glass, not the cowl.