Looks like a afun project. A couple of opinions:
1. I'd get rid of those goofy extra-long shackles.
2. A SOA conversion is a PITA and not necessarily cheap if it's done right and all the geometry is done correctly. I'd get a basic suspension (spring) lift and call it good.
3. I've run automatic lockers (with 4.56 gears) in both axles of my CJ7 for over 15 years without any problems. I'd avoid the expense and possible snagging of air lines with air lockers.
4. If you're contemplating running tires larger than 32", or swapping in a larger engine, you might want to consider changing the rear axle over to one-piece axleshafts or a full floater system. The former is much cheaper, but the latter is stronger and more versatile.
5. Converting over to a diesel is going to be somewhat of a drawn-out project. On the other hand, AMC 360 engines are still rather plentiful, cheap, and easy to swap in.