I think the inner cowl panels have to be one of the hardest panels to replace. Others please correct me if I'm wrong, but they connect to so many other pieces - cowl, firewall, inner fender, frame, etc. And the door hinges connect there with additional bracing. I appaulde you for replacing them and fixing up another E-Body.
There's been many a Mopar I passed on because it was just too much work for me.
I wonder if newer panels are better from AMD. Wouldn't hurt to call them, tell them what you encountered and if they haven't changed the panels, they might in the future based on your feedback.