J Crowder, I sense your frustation, I have been there myself. Had some great help from RODW (and others), and am happy to share my working Mesa 7i96 gantry style XYYZ cnc config with you
My XYYZ config (all files including .hal and so on)
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Originally my machine used two standard parallel BOB's. I wanted something more modern so I bought a Mesa 7i96 card (more in and outputs for example for my new control panel) and started of with a new config made with BigJohn's excelent 7i96 tool. I merged the two configs and am very happy how everything works now. I use gmoccapy and a touchscreen right now, also a xhc-hb04 for remote control. Gmoccapy does automatic tool measuring with each tool-change (and moves the spindle to a convient location to change the router bit).
My configs are not optimized and could do with some clean up. But it works for now and I am happy. I am sure you could use some of the settings for your setup.
BigJohn's tool:
gnipsel.com/linuxcnc/7i96/index.html
(much better then the pncconf that is supplied with LinuxCNC in my opinion.)