Windshield Leaks

My windshield has been leaking at the driver and passenger sides near the bottom of the windshield. I recently removed the windshield and rubber gasket to find out where the trouble lies. I figured there might be a hole in the lower a pillar, but what I found is that it was just a rusty mess at those lower corners and someone had previously tried to smooth out the area where the sheet metal is joined and spot welded at the factory. It looked like it was smoothed with bondo which had basically disintegrated. Once I wire wheeled out the bondo, I was left with what appears to be a leaded joint which is quite uneven and looks like it might not be sealing the factory sheet metal lap joint. Does anybody know if this lap joint was sealed at the factory with lead? Or perhaps this was a repair made later. The sheet metal appears to not be rotted through. I am considering removing all of the lead with heat and resealing the lap joint with perhaps Por 15 seam sealer, or fiberglass bondo which I understand is water proof.
There is another issue which I seek guidance. In the drivers side lower windshield area there is a small (5/16") square hole just below the dashboard bolt which is either some type of drain into the cowel or perhaps one of the places water leaks onto the floor during any rain. It looks like it might interfere with a good seal. Has anybody seen this hole before? It has some type of flexible piece coming out of it. I have attached pictures before and after cleaning.

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