I have come up with my game plan for attacking this problem. I have a 1998 with a stock intake manifold too so I don't have to worry about any sort of clearance issue just yet. Anyway, the cracks seem to stem from additional leverage on the exhaust manifold/header. I had a flex pipe installed in the middle of my down pipe, ordered a new Anchor transmission mount from RockAuto.com, and have a new set of Brown Dog motor mounts on the way with their ultra-flex rubber. Once those are in, I'll install my new APN header and hopefully everything will be squared away.

One thing to note about my flex pipe install. It appears that the new flex section being welded in has caused an odd resonance at about 1800 RPM. It almost sounds like a power steering pump working (in fact I replaced my power steering pump because of it). I'm hoping that once everything else is put together the resonance will go away otherwise I will be revisiting that part of it.

Good luck as this seems to be a long term issue for a lot of people. My Jeep is my DD and I plan on keeping it so I don't mind sinking a few into it to hopefully solve the problem once and for all.