Our Dana 44 front and rear axles from Drivetrain Warehouse arrived loaded with 4.56 gears and ARB Air Lockers. The ARBs have thus far performed flawlessly and our gears run smoothly and quietly. We did suffer leaking front and rear axle seals very early after the axle swap, however. The rears had moderate weeping and the passenger-side front was letting enough oil by to make a small puddle in the morning. We had TAG Motorsports in Escondido, California, swap out the leaking seals, but it required disassembly of both axles-not something we really appreciated, considering the newness of the units. Furthermore, our front axle was slightly bent when it arrived, most likely from when the brackets were welded on at the factory. the alignment rack showed a 3-degree difference in camber. it doesn't sound like much and we haven't noted any handling or tire-wear drawbacks, but it's enough to notice with the naked eye when you look at the front tires and is to what we attribute the premature failure of the front axle seals.
The TCI th700r4 transmission we swapped in place of the factory tf999 is a monstrously durable unit and has consistently delivered firm, crisp shifts. But we do perceive a loss of power with the larger GM tranny. It just plain takes more oomph to spin than the stock three speed. Even with our 4.56 axle gears, acceleration seems on par with the tf999 and 3.07 gears. we had planned for a GM V-8 swap (maybe an Ls1 or a 5.3L Gen III engine), but the factory 4.0L just keeps on ticking, so we're delaying those plans. Also, the mechanical linkage that connects the Lokar shifter to the tranny can give a slight buzz now and then, but it's not enough to make us swap to the cable operated shifter.
Finally, one thing we didn't really consider until after the tranny swap was the electronic aspect. Our TJ's factory ECU requires a signal from the tf999's lockup converter, so it would constantly throw the check-engine light on. Every time we cleared the DTC, it would reappear, and all efforts to bypass the problem failed. In the end, we wound up purchasing a $450 ECU for a manual-transmission wrangler to solve the problem. If you're starting with a manual-transmission wrangler, you won't have an issue, but be aware that you'll also need to swap the ECU when swapping out the factory auto tranny.