Probably easiest to use the Chevy version of the 231 and install the Jeep's short tailshaft (or a slip yoke eliminator) to shorten it for YJ use, no need for adapters, then.

The 700R4 or 4L60E OD automatic to match the year of the engine and electronics you use would be the best automatic trans. No adapter needed to the engine, of course!

Another option on the Manual trans would be the NV3500 5 speed. It's lighter duty compared to the NV4500, but it shifts smoother, weighs less and probably costs less, too. It and the Chevy NV4500 use a hydraulic clutch actuator, like the 5 speed you have now.

EFI, either TBI (Simple) or Tuned Port (more upper RPM power) would be the best induction system. OBD-1 ('95 and older) is the easiest to set up.

It might be best to buy a complete running 4X4 Chevy 1500 truck with all the components in place, maybe a rollover, rust-out or rear end total wreck. That way you would have the engine, wiring, sensors, trans and t-case in one package! You could part out the rest and recoup some of the cost.

One thing to consider is whether or not your states' emissions laws allow a swap and what procedure, if any, you need to do to get it to pass a smog test.