If you do still have the stock brackets , and not some other part that was just welded on, then maybe they are bent out and giving you the extra room.
Your shocks should be of the eye/eye type with the top and bottom eye being the same size. The upper eye does not use a metal sleave in the bushing while the lower one does. The bushing should extend beyond the shock eye by about 1/4 on each side. Thus fitting snuggly into the lower bracket whose outer walls are vertical and contain the holes for the bolt to go through. Does any of this fit what you have? The bracket is shaped like a "U" but with a squared of bottom.
1975 CJ-6 1983 CJ-8
1986 CJ-7 Laredo 1986 TJ-7 Trail Jeep
2003 Inca Gold TJ Rubicon