I think the hole you cite just forward of the vents must be where the control cable goes in, should be a grommet there, water in that hole would just be a symptom of the general deterioration hidden inside
the only way to fix the area is to find out just what's rotten inside and patch it properly - the way it should work is any water getting in the cowl inlet runs down toward the inside vents, but is deflected around them by a "gutter" sort of arrangement above them and carries on downward to a drain opening at the bottom of the cowl where the lower fender and the brace rod attach - over time the guttering inside the cowl can corrode and the drain at the bottom will get plugged up - this is particularly a problem when the truck lived in a dusty area and/or got a lot of trash [straw, leaves, etc] into the air inlet, and it was never flushed out, as in the farmer never washed the truck well .... also, it's likely the rubber seals are rotted on the flap that the cables control
fixing that area properly will usually require cutting open the plenum on the cowl that the back of the fender bolts on top of .... and if you want to plug the top cowl inlet, you'd have to make your own solid piece, and short of actually welding the piece in, you wouldn't be able to seal it well the way it fits and with the wiper towers poking thru
Bill
