Can the transmission actually shift into 5th? (right and up) If not then my guess is that it was originally an automatic and someone swapped in a manual. Unlike XJ's, YJ's were never offered with a AX-4 and even in XJ's they are rare. Personally, I'd consider swapping in a AX-15 or NV3550 if you're going to bother changing it out. No point sticking with a 4-speed unless it's a SM420, SM465 or NV435.
If you want to at least get stock 4.10/4.11's then I suggest buying a complete set of axles rather then having the gears changed. You'll end up with two spare axles for parts and you'll be able to swap the axles without having to deal with installing gears. The other option is to look for someone selling some axles off a YJ that are geared lower already. Maybe use it as a chance to upgrade to D44's. You can regear to 4.88's and be OK even with a 4-speed.
Although it does look good with those wheels, tires and lift.