yes, a pic of the damage would help, won't be 'topsoil', but very fine rust particles from the unpainted side of the metal, wetted by condensation or leakage - drying it out will only work til the next time you wash the truck or are out in the rain
the cowl is the firewall back to the "A pillar" [front door jambs] - the vent right in front of the windshield is the 'top of the cowl' - that air inlet feeds a chamber that goes both ways inside the cowl to the plenum boxes on each side under the backs of the fenders [the rear top of the fender bolts to the box], which in turn feed the kick panel outlet vents .... the bottoms of that cowl air chamber [below the side boxes] have a small drain so that water that gets in the air intake
should run right out [flush from the top with a garden hose and see where it comes out] - that drain gets plugged with rust particles, road dirt, evergreen needles and leaves - you'll probably find it rotten down there
further, the lower hinge pockets are close to that air space, and in turn collect water from poor door seals [the 'dogleg' is a bad design] ... if you remove the small kick panel covers and the inner louvered vent panels you can check it all out, more so with the fenders off - any holes you cut will have to be patched, "capable" or not

the assembly manual is a good reference, that whole area is a common problem for the series, the only patch panels available from the vendors are for the hinge pocket areas, the face and the pocket itself
Bill