interior & trunk water leaks

I would suspect the window gaskets at both. My brother's 66 has small pin holes in the window seam frame that had rusted out, that maybe you missed when you installed the windows. But you'll hear mostly that the gasket is your culprit.

You have to use GOBS and GOBS of the black butyl sealant to get a good seal. Between the glass and the rubber and between the rubber and the car. You might salvage this by squirting more of the goop between the glass and the rubber. Just lift the edge and stick the nose of the applicator down inside and squirt away, moving all along the sides and bottom