Cowl Cleaning

Well, I started on cleaning out the cowl today. What a freakin mess! I vacuumed as much as I could from the vent box holes inside. I duct taped a smaller clear plastic hose to my shop vac hose to reach as far as I could. Then I taped all the openings up and blew through one of the drain holes on each side with compressed air. Then I finished it off with water through the slotted cowl openings in the front of the windshield. I think I was able to get most of the garbage out. Unfortunately I found a couple more issues.

First, my windshield gasket leaks. That shouldn't be too big of an issue I guess. Just something else to put on the list.

Second, the raised "rings" around where the vent boxes attach behind the dash leak on both the driver's side and the passenger side. Is this a common spot to leak? I figure I can just scrape off as much of the old sealer I can, then just smear some new sealer over the joint. My question is, what type of sealer would be best for this application? I was thinking rtv would work. What do you guys think? Silicon, rtv, seam sealer?

Thanks!