Though I have a 67, similarly I only have some rust on the inside only. My cowl did check to be good & not the cause, and since the rust is only on the inside, and I know I had an airconditioning evaporator drain plugged at a time (or two), I believe it was caused from the AC system.
As far as what the original poster has (using his pictures) If it were me, I would really look at the cowl again by pulling out both fresh air inlets and looking around those areas carefully. If it IS the windshield (as also mentioned) there should be water witness marks or tracks visable, yes? Basically, again, I would seriously look for the cause and not just the effect, if it were me.
Richard