With everything detached from the transfer case, the nuts holding it to the transmission can be removed. With those out of the way, the T-case can then be taken out.
In this side-by-side shot of the Atlas II and our NV231, you can see that the Atlas is a bit bigger overall. However the rear output is actually slightly shorter on the Atlas than our NV231 equipped with a short-shaft conversion. This means you might need a longer rear driveshaft, which isn't a bad thing, since TJs have short rear driveshafts already. Compared to an NV231 without a short-shaft conversion kit, the Atlas allows for a 6-inch longer rear driveshaft, which is a major gain. If you look closely, you can also see that the front output on the Atlas is farther forward, which means that if you opt for this conversion, you will have to get your Jeep's front driveshaft shortened.
We also made sure to get the stronger 32-spline front output shaft on our Atlas. It is larger, stronger and will accept beefier yoke assemblies than the 26-spline output shaft that is standard. Advance Adapters can also perform the necessary surgery if you already have an Atlas with a 26-spline output and want to upgrade it to the stouter 32-spline unit.
 The next step was to put the...  The next step was to put the Atlas into position and to try to figure out its clocking. Once we had it lined up in the position we wanted, the case was marked so we knew which one of the four holes to put the studs in. |  With the Atlas back out, the...  With the Atlas back out, the mounting studs were inserted according to the markings that were made. Here you can see the different threaded holes for the studs that allow you to clock, or index, the Atlas. |  Next, we prepped the Atlas...  Next, we prepped the Atlas to be installed into the TJ. The Atlas uses this tube to help you tell where the fluid level is. The fittings for it come loosened. First we applied some Teflon tape, and then tightened them. |
 The factory four-wheel-drive...  The factory four-wheel-drive indicator-light sensor is removed from the stock transfer case and screwed into place on the Atlas. |  Advance Adapters suggests...  Advance Adapters suggests assembling the shifters on the Atlas before you install it to get an idea of how they go together and to make adjustments. This was a good idea, as once the transfer case is in place, access to the shifter assembly is a lot more difficult. |  Once the shifters are taken...  Once the shifters are taken back off the Atlas, it can be slid into place under the TJ. We decided to leave it clocked in the same position as the NV231. |