Hey Camino, I am very excited for you, while I can understand others concerns and so called bad vibes. I have loved these trucks and even on my 94 Suburban ran into the hing issue you talked about on the rear door.
For me, the gasket was installed wrong by GM on the assembly line and it focused water onto the hings and they started to rust. Here in Seattle where 9 months of the year is drizzel or rain, an issue like that starts rust fast, I was able to GM right at the end of the warranty to replace the seals and complete door. In this case, I would say you could probably pick up a replacement door, get it painted to match and put in new seals and have it solid and done right instead of trying to replace just the hings and weld it and then paint etc.
Personally, I love what I see on the truck and would strip it down to the frame, sand blast it, have the frame galvanized and then build it back up clean. You could pick up the Ramjet 350 to go in that baby along with a clean new wiring harness to eliminate any electrical issues. Best thing yet is that the new harnesses have all the updated connections so if you decide to add newer features you have the connections to do this.
In regards to the drive line clunk, I would say have a transmission shop give you a free review. At least here in Kirkland WA, there is an awesome tranny place where the owner will take the auto out and test drive it and then put it on the rack and check it out and give you an estimate of what is wrong etc. If you want to pay the $99, they will drop the tranny and check it out a bit more and give you an even further detailed estimate. I have had a clunk in my driveline and they found it to be at the connection of the driveline to tranny, pressed out the universal joint and replaced the neck as it had somehow become broken and once that was fixed it was smooth as if it was brand new. But I feel it will still be a minor issue for you once you get a good look at the driveline. Could be just a slip yoke issue, or spline stub end missing a few teeth.
It could be rebuilt to be really clean, OEM new looking and have a fun kick in the ass engine.
Looking forward to additional pics as you get started on the project. I would not worry about the internal stuff like the missing AWOL rear speaker covers, if you want OEM, those are easy to get still and really you could pick up some nice aftermarket covers that look even better.
Rock on with the new baby!