Some info that might help you decide:
Suspension & Engine Weight
You'll be replacing one of three factory engines. Their nominal estimated, accessory loaded weights are:
•2.8L V6, 365 lbs.
•2.5L I4, 340 lbs.
•4.0L I6, 515 lbs.
Engines you may replace these with may include:
•Chevy 4.3L V6, 425 lbs.
•Chevy Small Block V8 (Gen. I & II), 550 lbs.
•Chevy Small Block V8 (Gen. III+), 470 lbs.
•Chevy Small Block V8 (LS1), 407 lbs.
•Buick 90 degree V6, 375 lbs.
•Buick 60 degree V6, 350 lbs.
•Ford 302, 460 lbs.
•Ford 5.0L, 450 lbs.
•Ford 351 (Windsor), 515 lbs.
Factory springs are usually great for most Small Block V6 and V8 engines. We have replaced four-cylinder Jeep engines with V8's and noticed no sag or overly soft ride in the front axle.
^^^
I figured this is relevant since your running stock YJ springs.
This info came from the Novak site on their knowledge page for YJ engine swaps.
http://www.novak-adapt.com/knowledge/yj_87_95_swap.htm
http://www.novak-adapt.com/knowledge/fsb_swap_yj_87-95.htm
I would also ditch the idea of running an AX-15 behind a V8, there are much better options for manual trannys. If you go Ford I would look at an Np435 or T-18/19. Better 1st gear ratio and much more compact, giving you a longer rear driveline. For Chevy, SM420 or SM465. The NV4500 would be nice too for the overdrive, if you can fit it length wise. If this is offroad only or the majority of the time, I would stay with the older 4-speeds for cost and packaging.
For a ford engine, the C4 automatic is a great swap for a lighter rig like this. Its a 3speed, and very compact for an auto tranny. They can be built very strong, and are pretty respectable in good stock working order.
Another thing to consider, if highway time is a major parameter, is the engine RPM's you'll be turning at cruising speed. Most all of the early 4-speed manuals have a direct drive 4th gear (1:1). Given that, the 36" tire diameter, and the 5.13's in the diffs, you'd be turning over 3k RPM at 65 MPH.
That's a little higher than I'd wanna be spinning it, but its doable. Here's another link to the Novak site that can be fun to mess around with:
http://www.novak-adapt.com/knowledge/gearing.htm
If your not going to spend a ton of time on the road, the 5.13's will be fine. However, in a D44 that's a little on the steep side for V8 power/torque. Not to mention you'll have to be easy on the throttle to save the shafts too. It's certainly debatable if a 44 will hold up to V8 power, and I'm sure there are many folks who have had good success with it. I'd say you're right on the border line by running 36's, but compounded with the deep gears, it'd be and area of concern for me personally. Nothing wrong with running till it pops though (and it may never), I totally understand the value in running what you have.
Not sure what transfer case you're thinking about, but being driver drop, there aren't a ton of options. I'm not sure if an early bronco D20 is adaptable to the Ford 4 speeds, but should have come factory behind C4's. It's a good strong case and the EB version had a 2.46:1 low range (not too bad). The other option that sticks out is a flipped D300 which is pretty common. The 300 has a 2.62 low range. I doubt a full size case, such as a NP205, would be a good option for size reasons.
In general, I feel like its best to get your low gearing from the trans and t-case and gear the diffs to match the tire size. With a V8 you can stand to go with a shorter (numerically lower) gear in the diff, because the power and torque is there from the engine to get you moving.
In conclusion, there are lots of good options out there, hopefully some of this ramble will give you some stuff to think about. I have to say if it were mine, I'd go with a Ford 5.0L from a mustang, a C4 auto, and an early bronco Dana 20. That gives you fuel injection, cheap parts availability, lots of aftermarket support, good drivetrain strength with decent gearing, all in a very lightweight compact package. That being said, I'm not really a Ford guy or an auto fan, but that seems to be the best fit for THIS rig. Of course thats just my opinion...
Good luck and keep up the good work.