For a better fit they the holes should be filled with weld, ground flush, marked, and drilled.
Two of the holes line up. Two dont
Fill the holes that dont line up with weld and grind them flush
Punch those studs out of the axle housing
Bolt on the backing plate using the holes and studs that fit
Mark the holes that need drilling.
Drill out the holes.
Repeat the process with the 03 and up TJ/Rubicon retaining plates.
Re-install housing studs and bolt everything up.
I would be concerned with just wallowing out the holes, and personally isnt something I'd do. That basically leaves 2 bolts doing the work of 4 as far as holding the backing plate in place goes.
Im sure maybe it might be just fine, but its not what I would do.
Just my 2 cents.