Yeah, I think you're right, but a guy on FBBO suggested maybe trying a slightly longer 3/8" bolt first, so what the heck. I was putting in a 2nd 1/8" body shim at the time...so maybe I have some threads left.

If worse comes to worse.....what is up in that cowl area? (captured nut? threaded plate?) and how do I get it out?

Just to be clear, this is the top driver's door hinge...the half that bolts to the body. There are two bolts coming from the interior area into the hinge from the inside, and one bolt coming from the outside into the interior area....that's the one I stripped....otherwise I'd just repair/replace the top hinge... the stripped threads are up inside the interior/body/a-pillar/cowl area.