I've recently found the same problem with some heavy rain in Colorado. It happened to the passenger side and I had a bunch of standing water by the floormat under the dash. I called and raised hell (erroneously) with the rack store, because I had JUST installed my aftermarket roof rack. Anyway, turns out that it's not the rack, and I think it's coming in the same place, by where the fender meets the firewall.

Incidentally, those custom subs are incredible, man. Don't suppose you have an extra set laying around, do you?