Hey Jeffy,
I have been having the same issue (wet drivers floor board 
) and couldnt figure out where its leaking if my life depended on it. Is there any way you can explain to me where this drain is located.
***I have a TJ is that makes a difference 
TJ's actually had a TBS on the leaking issue from the cowl. You'll have to go to the Dealer and see if it was done though. They can look it up. IIRC, they cut the length of the drain tube off. But since there is a TSB, you might as well see if it was done.
i see what you mean - i was thinking to make a piece of alu sheet and fit it over the heater intake but from what you are saying it will still leak once there's enough water in there - although i did look and there is none when raining, seems to be draining out (could be that is actually draining inside :) - since my Jeep is standing still at this time i'm just going to block the cowl vent and see if that solves it - if it does i'm going to buy a scoop like you suggested - this has annoyed me since like forever.
The way I was able to tell were the leak was coming from was by looking at the firewall. After a good rain there is usually still some drops on the firewall. I'm sure it's not draining out into the floor but more like constant splashing Even with the addition of the little wall, I still get water in there. I'm not sure if it's getting into the passenger side duct but there is a vacuum controlled flap on that side. The duct height on the passenger-side is about the same as the driver side but it's a lot longer and doesn't spill right onto the floor. Sealing off the vent will help you localize the leak at least.
I need to get a new windshield gasket for mine, it's leaking like mad in this weather. It SUCKS! The other morning it poured a steady stream down the dash from my driveway to the stoplight a mile up the road from my house. Since then it hasn't leaked nearly as bad, but still leaks...
And my soft windows don't work that well when it comes to sealing with the hard top to stop leaks... And my back window leaks...
My Jeep sucks in wet weather
I did mine a few months ago. It's a bit of a PITA since the new seal is a lot thicker then the squished old one so you'll have to re-adjust jsut about everything to get it to fit. This is more of a PITA if you have a hardtop. Also, I think I get a little seeping where teh wiper motor cable is passed under the seal. It's not much like the HVAC duct but I do see traces of water on the instrument panel.
I´ll again suggest putting some sort of sealant on the screws that fasten the cowl vent. Mine kept leaking a bit until I did that and it can be pretty hard to tell if it is the screws of the vent since it can leak into the same general area.
My leaking is distinct and you can see the leaking on the wiring and firewall. It's not the screws as there would be leaking down the HVAC duct and onto the transmission hump. I'm getting water dripping above the throttle and there is moisture on the tab under the duct flap since that's the lowest place for water to travel.
