I doubt it, but you probably can do a lot to eliminate some of them.

You're probably on the right track on welding floor and toe boards in eventually. Glueing the windshield frame in will probably help. If I was worried about it I'd probably use some anti-squeek strips between the fenders, body and running boards and same on the fenders to nose. insulated sound-deading on the floors and in doors will probably help to, along with eliminating the original window regulators like I think your planning on. Then there is the tailgate; eliminating the chains will help, and some kind of seal between the body and gate will help, but it will be hard to get rid of the rattle at the hinges when you hit a bump.