Well, I think I know what the boxes are now... and feel kinda dumb now. I think (haven't gone back out and taken off the grill again) they are just the drains for the air intake nozzle, to help keep rain from getting all the way up the tube.

Was sitting thinking of how to keep water out if I make the tubes bigger and remount a filter and it suddenly hit me, that's what they had to do and thats why it has a 1-way flap.

duh