If you want to keep a manual transmission, which I would, a T-5 swap is a good choice. The SM420 4-speed (I have one) in my truck with a 250 6 cylinder and 3:73 rear means my truck maxes out at 60 mph on the highway. The T-5 (which is what I plan to do, although a T-56 6-speed is also appealing) is in my plans.
As for body work, I'm in a similar situation, although probably worse since I have to replace every body panel in my truck except for the front bumper, grille, cowl & side cowl panels and bed sides. Everything else needs to be replaced. If the truck hadn't of been in our family for 30+ years I wouldn't be restoring this truck. However the nice thing about these trucks is that they are relatively simple and easy to take apart.
What are you final plans for the truck? Nice driver? Frame-off project? Budget also has a lot to do with it, body work is expensive. Although I'd rather do mechanical work than body work any day of the week.