First would come the engine, next the trans. With the power of the driveline, why keep the stock aluminum chain tcase? Swap in an aftermarket $2000 case. Then swap in rears to handle the torque and hp. Swapping in big diffs requires big tires to clear. To get the most out of the tires, you'll need different than stock suspension.
So in overall cost, might as well keep your 4cyl Jeep, wheel it, gather together pieces to get your hemi Jeep together. Sell off the 4cyl Jeep for a bank to start assembling your hemi Jeep.
Review 4x4Xtreme. They did this particular build in a few weeks without a budget. Wrecked TJ, swapped in Hemi driveline, D60s front/rear, gears/lockers, coil-overs/long arms, stretched wheelbase, 40s, aluminum beadlocks, and wheeled it in TN for a couple of vids.