Hokay, we begin with the removal of the problem child first.  If you don't know how to do this, then you shouldn't go any further with this install.

Support the tranny with a jack (we usually add a small 2x4 to the top to spread out the weight).  Yank of the center skid, lose the driveshafts, and remove the linkage.  Try not to tip the old t-case to much or removing it will become a lot messier than it has to be.  Get it down off the tranny and put it in the corner of the garage with the other discarded useless cases.

You also need to go to the inside of your Jeep and take out the front part of your console so you can make room in the floor for the shifters.  Pulling your driver's seat will help a lot also.

To remove the transmission shifter handle, just simply pull up on it really hard and bust your hand on the dash when it finally pulls free.

The airbag safety stuff, pops up from the clips holding it on the bottom side and then you can put it back through so you don't have to disconnect anything.

Now it's time to just sit around regarding the new shiny replacement.  Even though the Atlas is shipped dry, ours seemed to be oozing something we believed to be plain straight testosterone.  The packing of the unit is cool too because the Atlas is basically just foam sealed in its box.

 

 

Go ahead and root through the parts to make sure everything is their and to familiarize yourself with them.  Our package was missing one of the all thread studs, so we just picked up a piece of grade 8 fine thread ready rod at the store and cut it to size.

You need to begin assembling the shifter tower and linkage before installing the Atlas.

Locate the 3 hex hex bolts.  Apply Blue RTV to the threads and install the aluminum shift tower to the Atlas.

Install the large all thread into the shift tower with the jam nut to keep in place.  Slide the extension tube (small length of pipe) on the all thread over the jam nut and it should seat with a little tapping, on its spot on the shift tower.  This extension should put the shifters where they need to be to come up through your stock shifter hole.

Take the small all thread rods and thread on the "shift tower" buttons.  The diagram states to place a heat shrink tube in between them, but if you are installing your atlas in a wrangler as we were, you use the provided O-rings to keep the buttons from screwing further down the all thread.  Add the small nyliner plastic sheaths to the button ends.

Put Teflon tape on the Atlas's threaded shifter rods.  Then screw on the brass ends until finger tight and then back off enough for alignment.  Also add tape to the threaded hex bolts that will hold the shifters in place.

 Now, by looking at the diagram, assemble the rest of the shifting linkage up against the extension tube.  You want to adjust the shift buttons on their all thread links so that the shifter handles stick straight up from the tower.  Once you're sure of where you want them, add the c-clip to hold the buttons in place.  You can add the grease fittings to the tower also.

You might as well now take off the old components off your old t-case that you will be reusing on the Atlas.  This includes the 4x4 switch and the speedometer gear assembly.  Reinstall them and then remember after the completed install to hook all of them back up.

 

 

Okay, now comes the first of many tests.  Get the Atlas on a nice stable jack and ease it on up into its spot behind the tranny, carefully guiding the shifters through the floorboard. 

There are a couple things you need to measure for and figure out now.  First, you're going to have to cut away some of your floorboard to make room for the shifters' travel.  We cut away more than an inch up front and ended up adding some sheet metal to the rear to keep the heat out of the interior.

 

The second thing you're figuring out is what height you are going to clock your Atlas at.  Obviously you are mounting the Atlas up against the tranny, but for each stud that will be making that connection, there are 4 different holes you can use.  This way you can rotate the Atlas until all your clearance issues are met.  Figuring out which hole to use is not a fun part, but it is an excellent way to be able to chose how you install your Atlas.  One of the reasons Chris went with the Atlas was that he could get a longer high angle driveline and eliminate the transfer case lowering pucks that also lowered his ground clearance.  By using a shallow rotation he could bring the canter skid back up to where it should be.  We went with the second hole giving it the second shallowest position because at the shallowest he would have to cut away some of his floor to make room for the huge Atlas.  At the second shallowest, 14 degrees, it is closest to the original's 13 degrees, and fits just fine, as long as you cut out a section of your center skid.