Ah well im hoping this was my only issue, made it through the last couple rains without any issues so i hope it stays that way. Otherwise i see it as a funky design for the air intake box, it looks to have about a 1" plastic/rubber drain hose in the front corner towards the motor, that looks to be there to drain out the water that comes in the hood vent. My hose was in like a pinched position as well, and looks like it would prohibit water from exiting that air box in the way it was meant to.
If that hose on the bottom of the vent airbox is pinched or obstructed, and doesnt allow the water to exit the box, it will fill up the 2" over the lip of the circle air intake, and flow down the vent and onto the floor via the 2 duct connections in the passenger dash area. I think this may have been an issue at some point as well on this car, since there was water stains inside of the ducting when i removed it to do the heater core. Figure its worth checking, water can only get to that floor by a couple of routes.