For the drivetrain, the first thing I would do is ditch those 3:90 gears for something taller. I'm not sure what all you can go with for your housing, but look for a ring and pinion in the upper 3:00 range. It will make a difference. Start with the simplest item first, I say. Not to say slapping in a ring and pinion is super simple, it's just easier than doing a T5 tranny swap.
Now, as to the body, I do have a recommendation and this is coming from experience. My '71 is my daily driver, I can't have it down for long periods of time, it's the only running vehicle I have right now but it does still need a ton of body work, much like your truck. I am starting on the back. These last few months I have lined up lots of parts. I have nice bedsides to replace my beat to pieces ones, I have a nice tailgate in storage, trailing arms on the way and am buying all the small parts. I will take a week of vacation this summer and strip off the bed and do the whole butt end in that time. This project has been months in planning.
Next up will be the front. I am in the process of getting some quarter panels and inner panels worked on and have a nice hood in storage. Then comes the question of the cab. I have the same dilemma as you. In my case I have gotten another cab. I am going to have that one worked on and fixed up, then next year (hopefully) I will take a couple weeks of vacation to strip off the cab and front end and put the fresh parts on. It will be a bit of a pain with registration since the VIN will change, but it will be fixed up. It may be something for you to consider as well.
I know it's a long rambling post, but I hope you have gotten some ideas anyway. Good luck on your truck!
