cowl repair

I've been driving the car like this for a while now and it hurts me every time I look at it. The cowl hood came up (my own mistake) and it bent the cowl panel assembly, broke the plastic vent cover and the passenger side wiper arm. I did a search on the forum and couldn't find anything useful...

I am pulling the top of the cowl off on Monday and wanted to know if anyone has any suggestions on how I should prep and what I should use as far as future protection?? After replacing the cowl vent collar, my plan was to treat the rusting surface, prime and the apply undercoating. Any suggestions?