Better the windshield than the cowl. Most often the windshield is the problem cover the cowl and spray the water then check for leaks.
Marty, that's what I'm afraid of too. I am beyond frustrated with the windshield design on these cars. Every '65-68 Mustang I've had leaks, except for the one my dad bought nearly new and has never had the windshield out. How in the world did Ford keep these things from leaking when they were new?! There's nothing worse than welding in new floors and installing new sound deadener and carpet, just to watch it all get soaked the first time it rains. Sorry, just had to vent!!