any tips on cleaning out the cowl?

Would it be ok just to seal the cowl vent openings. I would be using an aftermarket a.c. system. Or is that asking for trouble. Please no laughing :)

If you're talking about sealing the holes on the bottom side of the cowl, you're asking for trouble. If the cowl stopped draining, it would fill up with water and you wouldn't know it.

If you really wanted to eliminate the inside cowl vents, the best way to do it would be remove the upper cowl vent opening (the grille behind the hood) and replace it with sheetmetal. Of course, your A/C would have to be able to recirculate cabin air for that to work, there'd be no fresh air intake on the outside of the car.

I would like to know this also. it's been raining and i have water gushing out of the boxes

That's because the cowl isn't draining properly. The inside vents have a raised lip on the inside of the cowl, if water is coming in it's because the cowl drains are plugged and the water is coming in over the top of the ~1/2" tall lip. You need to clean out the cowl and drains. Either that or the lip is completely rusted out. Courtesy of 66Dvert from earlier

What the inside of the lower cowl should look like. The lip should keep water from coming in the vents....



What can happen if crap sits in the cowl for too long. Water would definitely be coming in the vents on this one. Plugging the vents would not fix this!



Here's another one from another thread, showing a rusted out lip on the inside of the cowl...