Leaking fresh air box??

Your seals are fine. Inside the cowl area are raised ridges around the fresh air drops, probably 1" high or so. You can feel them if you reach in there. That means your cowl is getting 1" or more of standing water in it; so that means your cowl drains are plugged, most likely with leaves and other incidental debris.
The drains are located on the sides of the cowl, behind the fenders above where the hood hinges attach.
Fish some wire or something similar up the drains while flushing the cowl with water from above through the grate; you'll know when it frees up. Try to flush as much as you can out of there, then repeat on the other side.
It would be easier to explain with a pic, but I don't have one handy. Maybe someone else has one they can post up.