there are drain holes below the hood springs, that if clogged
will drain water into the floorboards/underdash. your "patch"
sounds like you plugged a drain. unless you have rust holes,
you plugged what need not be plugged. oval, about 1/2" long?
working up from under the wheelwell, with a stiff wire/coathanger, clean out the lower drain. blow the whole hinge
area out with compressed air.
the windshield gasget should be symetrical. my experience is
that if you have a windshild leak, it shows on the windshield.

don