As far as I know I'm the only guy on this forum running JK axles. Check out mallcrawlin'... There's a guy that goes by Zombie who did a nice job with his 5.9
The following is part of one of my posts on another thread...
The XJ D44 is a light duty housing and is not much stronger than the D35. The ring and pinion are stronger, but that's all its got going for it. The shafts are slightly larger, but the same size shafts are available for the D35 in the 30 spline upgrade kits that are out on the market. Its also narrower than most of us need. Everyone keeps saying they're the perfect width but, in reality, the fact that the JK axles are around 5 inches wider, means they fit perfectly under a ZJ. With stock width ZJ axles, you will need spacers or aftermarket wheels. I have JK axles with stock JK wheels. Less wear and tear on the bearings. The total width is about the same as stock ZJ axles with aftermarket wheels or about the same as spacers and stock ZJ wheels. The rear axle housing is much more rugged than a XJ D44, with bigger, thicker tubes. Its got bigger (disc) brakes. 32 spline axles. Ring gear is 10mm larger than ALL other 44's and pinion gear is D60 sized. 4.10 gear ratio. Factory electric locker with simple 2 wire 12v hookup. ABS will hook right up too. Brackets need to be installed but, same story with the XJ D44.
And for anyone who may be interested, as far as the front axle is concerned, the tubes are still small like the TJ Rubicon axles. That's easily fixed by a truss and/or sleeves. Everything else is beefed. The axle also has the larger gear set like the rear axle but in a high pinion version. In my opinion the gears are as strong if not stronger than a D60 gearset. 4.10 ratio. Electic locker. 30 spline inner axles and 32 spline outers. Hybrid 1350/790 u-joints. Larger unit bearings, and they're a captive bearing design. Larger knuckles. Cross-over steering setup. Factory scrub radius makes it effortless to turn 37" tires. ABS hookup. Larger brakes. Factory control arm locations work perfectly with the ZJ. Track bar bracket will also work. Shock mounts are 1/2 inch out board but will still work. You also eliminate the need for bar-pin shocks. The factory spring mounts work with ZJ springs but are 1.5 inches out board of the stock ZJ locations. You can relocate them or you can leave them alone and relocate the ZJ's upper spring mounts out, each by 1.5 inches. I moved my upper mounts on the body. I figure the extra stability can't hurt. So that leaves having to rework the sway bar mounts. No big deal.