Guys i have been chasing this annoying issue for a while.
Have had my 04 since new.
Last year or so during a heavy storm my passenger side floorboard will literally flood.
I thought it would be easy to find the source but alas i i really can't pinpoint the source of entry.
The windshield cowl is vented on the driver side but not the passenger side.
Has anyone ever seen this issue and if so what was the fix?
Beers on me if you can help me remedy the cause!

 

Hey there... leaks can be comparable to chasing your tail....
I saw in here an alteration to the door seal, done by inserting some medical tubing in the channel of the existing door seal...

It was flagged as going into the tech folder... Have a look...

If it isn't the door seal then maybe the glass is leaking in....

I'm unsure but the tubing insert is an inexpensive way of checking the theory.... also eliminates wind noises and improves the "sound of the closing door"....
gl

 

My 99 F250 leaks on the passenger floor board as well. I think it is a seal that rotted either on the frame or door itself. I know there are a couple threads on noise reduction you might try that first and see what happens. GL and post some pics of your issue if possible

 

Ok, had this problem on my 01 F350, had to put some black caulk above the pass. side windshield in the rain groove ( ) you'll see it, and then, make sure you park with the nose up. My glovebox would be full of water, I am guessing the windshield rubber just shrinks and leaks.