water comin in through heater ducts

Well, those towers can rust out - and it would be some major surgery to fix.
I would start by removing the wiper arms and taping off the inlet grill and wiper shaft completely. Then, a water test of the windshield starting on the lower edge, then moving up the A pillar 1/2 way, at the top of the A pillar and then along the top. If you determine the windshield is not leaking then move to the cowl area. Clean it out thoroughly as Oldmanmopar explained. When it's clean, redo the water test.
You sound pretty positive the tower area is rusted out. Can you see that it is?
C