It's a pain and I"ve been told the only way to fix the leak is to replace the cowl. This is a massive job and involves drilling out hundreds of spot welds. One enthusiast counted them one day I remember being shocked at the number of welds that need to be drilled.
Anyway, I have seen a specially made clear plastic cover that is fixed on the external cowl vents that seals the cowl area and stops the leaks! It's only a bandaid fix but it stops the leaks if your happy to see it on the vehicle . Not sure who supplies these plastic cowl seals but I'm sure someone can point you in the right direction. Alternatively , if you are handy, it's just a piece of clear Perspex with some foam around the outer rim fixed using a T clamp & a small nut & bolt.
I"ve also heard of a plumbing sealer type substance used to repair leaky pipes can be poured into the cowl from the outside vent but this seals small holes ONLY ! I haven't tried this because I ended up selling my 65 stang.
Jake