The cowl/vent box drains to both sides of the cab, behind the fenders. If you remove the top cover, I'm betting you will see a bunch of crap and a small lake, on the vent box floor. open the drain slots at the rear edges on the sides to drain the water and then completely open up the slots. The water sits in the box and runs into the cab through the vent housing.

Might also want to check the drains on the bottom of the doors. The window sweeps are usually junk and water enters the doors along the windows. if enough water builds up, it will also empty onto the floor boards. The water filled vent boxes and water filled doors are 3 for 3 on my early 90s (90,91 & 93) Dakotas. The 93 was so bad, I drilled a hole in the floor pan so the water could run out. Gene