I'm hoping that's it. I crawled in the floor and looked under the dash while my son sprayed the windshield sealing area. I saw no water come in.
I had one rot out in the area right above the kick panel. It was hard to see until I pulled the fender.
I recently had my fenders off. My cab has no rust. The only good thing about living in the south. Plus both front floors are full of water. It's not just one side.
Run it through ant auto wash while you're in it. See if you can see or hear where it is coming in. The time and pressure from the carwash should reveal the leak. Unless it's in the fender like snoranger mentioned. Pull the floor liner out to see if it seeps in from the bottom.
I'm going to try this later today just for sh!ts n giggles and see what happens.
Mine has a small leak around the top corner of the rear window. I just need to get some dega seal and seal it up b/c I don't have the time or money to pull the whole glass and put a new seal in it. You could do a leak test by getting a really strong fan and mounting it to the rear window if you have one or one of the front windows, seal it off really good around the fan and window so it is mostly air tight, have the fan facing inward so you are pressurizing the cab. Now turn on the fan, close the rest of the windows and doors and start spraying the outside with soapy water. If your fan is strong enough and you have a serious leak then you should be able to bubbles somewhere. Normally if there's a small leak you can't find then this is the best way to find it. We use this method on 35' RV's with just a single fan and can find leaks all over. Plus its more than likely a free test if you have a strong fan and some time.
The back hump and floor of my truck is bone dry. I know my rear window has the drips, it's not enough to wet the floor. It just barely dampens the top of the back wall carpet panel.
Right now, I am looking for a good windshield to replace the one in the truck. My GF followed a gravel truck to close and picked up a few pockmarks which have run due to the cold and snow we had back in November. I'm also going to remove and reseal the rear window. On a 2001 standard cab where is the airbox drain located? I thought I knew where it was and through I was cleaning it out. I may have mistaken something else for the drain. My eyes aren't so good. Don't get old fellows.