With the body back on the jeep, the axle upper link mounts are about 2" away from the floor of the tub when the upper links contact the rear passenger footwells. That's a lot of potential travel lost. I can do a few things...
Dimple the floor like wildman said (or let the links self clearance from use.) I'm not sure the body can give 2" before pinch welds start coming apart.
Move the frame-side upper mounting points rearward. My upper links are currently slightly longer (as viewed in two dimensions from the side) than the lower links, so I have room to work with.
Likely a little of both will be the solution.
Things I've got to consider...
I would like to get the axle upper mounts all the way to the tub floor at full bump, but on my 3 link rear, the driveshaft would bind at full bump. So it may be pointless to get all of that up travel. However, my new driveshaft is going to be considerably longer, so maybe...
As
@NashvilleTJ had said, it will likely be the tires and body that dictate travel, so trying to get the axle all the way to the tub may be pointless