I've attached my ini and hal files for my gantry CNC router. It's a dual-motor gantry running 2.8~pre with Joints/Axes. It homes my gantry properly, and I've been able to adjust the two home switches so the machine squares itself up very well while homing. This only works with the current dev/master version of LinuxCNC, and not with 2.7 or any previous version.
Much will likely have to be changed for this to work on any other machine, but as an example it may be helpful to someone else who is also trying to figure this out.