Keep in mind that raising the shock mount on the axle will shorten the amount of shock compression available, while at the same time limiting the extension. You need to remove shock and flex the jeep...measure the maximum compression (against the bump stop), and extension to figure the shock travel needed.
I used to think the shock bracket hanging down below the axle was a problem, but I can't remember ever hitting it on a rock since it's so close to the tire anyway. Was never really an issue in snow (it's a small area and doesn't cause much drag), and I don't do a lot of mud. Might not even be worth the hassle for a little more clearance under the axle?