Update time. I relocated the clutch master cylinder an inch lower on the firewall (back to factory location) and I think the clutch issue is all figured out now.
My bodyshop guy came over the house last week to check out the truck. He'll be ready to bring it in for body work and paint probably within a week or two.
In the meantime, I am getting it ready for him. I removed the front valance, interior plastic, back window, etc. Unfortunately, I broke the acrylic rear window. So I am having a local window shop make me a new one.
I let me wife and friends give some construction criticism on the bed floor and they suggested I finish off the bedsides with sheet metal. I'm glad they talked me into it, because it looks a lot better.