i have done a few of these atlas/belly up conversions.
it is a great conversion, and money well spent.
luckily for us yj owners we have less sheet metal in the way, and can most often get by installing this without much body lift.
joe got off easy on his, but does not have the belly up on his rig yet.
the MMl and BL will help a lot. you can make up for it with a saw, or a few swings with a BFH. to get it FLAT you will have to put on the BL and MMl though.
you can have less than flat, i believe it is a 1" drop on the center skid, and the atlas at 7* without the bl, but what fun is that?
be SURE when yu order your atlas that you SPECIFY that it have a flat orientation or you will get one with a 7* rotation. this is important. i kick myself in the *** for not knowing this when i ordered mine.
you will ahve to shorten your front driveshaft, and lengthen the rear driveshaft, so be sure to add this to your budget.
i have some pics of my atlas installation on line HERE
when i did mine, as i said, i have the 7* rotation on it, which takes up room under the jeep making it virtually impossible to have a "flat" skid under there.
to help with this issue, on the 1" drop nth degree tummy tucker, i mashed a big dent into it to clearance for the atlas.
bear in mind that i DO have a body lift and MML. it is the rotatation of the case that kicks your butt on this thing.
i have the Atlas II 5.0 in mine, as does Joe Dillard. it is a great case, but you pay for it.
ask away if you have any questions.