Third Generation F-Body Message Boards

I recently started fixing up my 83 Z28 and the first thing is the rusted out toe kicks and floor pans. I've removed all of the dash and carpet on the interior, and starting with the passenger side, removed the heater/ac box and front fender. I don't want to have to do this again for a long time so I traced the source of the rust to the clogged up cowl drains. That being said, the seam sealer between the cowl and firewall failed, and boom, rusted out the floor pans. I definitely want to fix the rust, but also address the underlying cause so this doesn't happen for another 36 years or so. I plan on using this car as a daily driver, and I don't want to be shuddering every time I drive it in the rain.

For the most part I can see what needs to be done, except for on the sides of the top piece of the cowl, in front of the front corners of the windshield there are vertical seams where the cowl piece is spot welded to the top of let's call it the inner fender. There are gaps in the metal in a few places around this seam that look large enough to seem like they are intentional, to let water coming off the windshield join the rest of the water inside the cowl drain. Problem is on my car they've been filled in with some sort of pink putty. My question is then is this putty really supposed to be here? Without it, water will drain nicely down into the cowl and run out the cowl drains on each side of the car. With this putty here, the water now pools up there, and runs down into the engine compartment, and has rusted out the seam between the inner fender and firewall.

This picture shows the passenger side looking from the front of the car towards the back. The two circled areas were covered with putty until i scraped and chipped it off.
https://cimg0.ibsrv.net/gimg/www.thi...51780b8c65.png

This picture shows the undisturbed driver side with the holes plugged with putty. Particularly troubling is the (not pictured) electrical components mounted on the firewall just below this area that are getting completely doused with water running off the windshield and cowl.
https://cimg9.ibsrv.net/gimg/www.thi...5eb4958bd5.png

You can also see in the second picture, where the wiper arm is attached, it looks like they slopped a bunch of putty over that as well in what was I'm guessing an ill conceived attempt to dry up the floor. That doesn't make much sense to me since plenty of water is supposed to end up underneath there from the vents in the cowl.

So as I asked before, should that putty be there to clog up those holes? I'm thinking no, since about a foot to the right of them is a giant vent hole into this area that water most certainly will flow into. Also, what do you recommend as far as rust proofing the inside of the cowl area that the water flows through? There is plenty of rust in there already, and I'm planning on cutting out what I can and welding in patches and seam seal and all that to keep water out of the interior of the car. Given that this area is designed to have water flowing through it, I feel like I should do a little more than just scuff it up and spray it with Rustoleum.