Yes, go with Brown Dog. You don't have to go with lifted mounts, which would likely necessitate the body lift. And their bracket replacement kits should be the ticket to get that mess straightened out.
I just installed Brown Dog mounts (1") in my Jeep two weeks ago and they're awesome, and the folks at Brown Dog were great to work with. I ended up spending extra on the rubber bushings to reduce tub vibration.
You'll be happy with your choice.
01 TJ,HPD30/D44,OX,4.88,35s,1"BL,1"MML, 4.5" lift,OBA,Novak Shifter,Teraflex ESS SYE, UCF tummy tuck