After reading all that it still looks like a true fix has yet to be determined. I think the idea of adding some flashing to the top of the fresh air intake is an option. The real question is, "Is there supposed to be a snorkel type attachment that snaps over the opening to keep water out?".

Next time the cowl is off I will take some photos to post and if I find a fix I will post it as well. I have a feeling it has something to do with the channel in the plastic cowl cover that the rubber seal seats in. I think the plastic is not putting enough pressure on the seal there by letting the water flow past it and drip directly into the fresh air intake vent.

I think that removing the cowl and duct taping a piece of cardboard to the opening to seal it shut would be a start. Then you could replace the cowl and seal and leak test the cowl and seal without soaking the floor. The cardboard would get wet and help to figure out the problem. If the bottom of the cardboard is all wet then you know the drains are clogged. If it is streaked from the top to bottom then you will know that the seal and cowl have failed. If a leak is still present with the vent sealed with the cardboard and duct tape then at least a guy would know that it's not the cowl and seal.

I would love to be able to figure this out on my own, but they will not let me work on my car in the complex I live in. Which sucks.