This has turned into one of those never ending projects.
On the older Jeeps the body mount bolts do come down from the top, mostly from inside the tub. 6 are carriage bolts that needed to be tacked down to stop them from turning. Then there are the 4 in the rear behind the gas tank. The good part of that is I can pull the bolts so the lift won't be near as high as feared. The PO made a rear cross member and rear shackle mount welded to the frame with big ol' steel plates. Ugly from underneath the Jeep. The rear member is a 4"x2"x1/8" tube that isn't quite strong enough for the tire rack, but it's biggest sin is making the 4 rear body mounts almost impossible to get to. EEEERRRRRRRRRRRR!
After stewing a bit on the matter the easiest solution was to get the angle grinder w/cutoff wheel and cut a window underneath the mounts. Works, but the grinder rained hot metal down on my arms, thousands of little burns. The arms are not happy about it either. I won't leave it like that though. The metal pieces will get a nice round hole drilled or cut in them, then welded back in place and smoothed. Nobody will easily know what happened.
All this just to bring the front fender and the fender/hood gap down where it belongs. It's more than likely that nobody other than me will even notice it. But the cool part will be when standing around with other jeepers bragging about their lifts I'll be able to say, "Yeah I've got a 3" suspension lift with a 1/2" body lift." I can just see them looking at me like I'm the biggest jackass they have ever seen.
This whole project has been like this, frustrating. However I would be lying if I said it hasn't been great fun. I'm doing things I've never done, it has been great fun figuring out how to get through problems both expected and unexpected. and enormously gratifying when another Jeeper stands back smiles and says nice job, I like it.