Re cowl, I got into it as best I could from all accesses - in cabin lying on back (seats out), reaching up thru the duct holes, thru engine bay oval holes, and thru drain holes behind fenders. After cleaning (scrape, vacuum) and chemicals (rust removers), I painted the innards using rust-converter primers and paint, using sprays, mini-roller, and paint pad on a stick. Chevy guys have it easier with a removable cowl cover. Ditto for my 1985 M-B.
Re body, look for bulged areas in the pinch welds at the rocker panels. Those form open drain holes, but are often covered with undercoating. Behind the rear wheel, there are special round plastic plugs with a bulged drain hole. Insure that is open and someone didn't install a blank plug with no hole.