One thing before you purchase the axle, is to make sure your choice of gear ratio is available for both the front and rear axles. Then, I'd suggest to make sure the gear ratio chosen will work in real life scenarios, meaning the ratio will work with the speeds on the road you will be driving, especially if the Jeep is dd to work during the week, and 1-2 weekends on the trails. Trailriding can be compensated through other ways like t-case gears, doublers, or with different tcases. I know the choices of tcases are not abundant for the short wheelbase Jeeps, but there are a few. Cost is another thing in making these choices. With the gear ratio being changed, look for lockers to add.
For choosing the Rubi D44 for the front axle, the biggest impact is only the R&P size. Although I think the rotor is slightly bigger. The 297/760 series u-joints are the same u-joints used in any 1/2 ton and 3/4 ton (light). No difference there. With the front axle, its rare that the splines of the axle would be affected. The joint usually breaks first and if done properly, you can also take out the splines of the axle shaft and the side gears in the locker with the break of the joint.
If I had a choice of building a front and rear axle combo, I think I would look for a getting high-steer for the front, manual locking hubs on both axles, large discs, and width to fit wheel/tire combo with front slightly wider to provide better stability. I know of couple people who took a D44R housing, added D60 knuckles, and used D60 knuckle out combos (shafts/joints). They run manual lockers (ARB, OX). The shafts are high cost customs as well as the joints. They don't drive them too often on the street and always trailer them to the trails. Run 39's and 42's with v8s, auto, steep gear cases, 4.88s, and matching ff rear axle. 1 is in MN, the other in OR.
