Howdy and welcome aboard! I can't help with everything, but I can name a few. Removing the in cab tank will help with some extra room for sure. I have seen a couple builds where tall guys like you have actually extended the rear of the cab to add leg room. You could still put a fuel tank where the under bed spare goes and have a filler on the fender.
A 200r4 or th350 will bolt right up to a 250. Anything that will bolt to a 60's and 70's SBC will bolt up to a 3rd gen 6. You will need a flexplate and torque converter. Also the drive shaft will have to be shortened. Being that you have 3.07 rear gearing I'd do a th350. Most common automatic.