You will have to pull the windshield to better assess the damage done. Eaglegirls' SX/4 had the same issue. After removing the windshield, I sandblasted the whole pocket, that exposed a few pin holes. I know my fix isn't the correct way, but, I didn't have access to a parts car with a good cowl. So I mixed up some fiberglass reinforced body filler and gave it a skim coat in the bad areas. It was only pin holes, so not a huge deal, if you have severe rot, best bet would be to either cut a cowl out of another car, or if you are a decent fabricator, make patch pieces. Either way you go, It's no fun, Cutting out the cowl is a project, making patches, would likely be easier. On a side note, so far my repair has held up perfectly fine, though I took extra care to douse the underside of the cowl (accessed through the wiper motor hole) with paint, however her car does not see winter, so take that into consideration.