The re-wire is complete. The hard stops are now wired with shielded cable. With Nathan's help I put female connectors on all of the wires, as well as extended them so that the arduino and grbl shield would be off the chasis of the machine.
I could not find mushroom switches in the boneyard, so at this point what still needs to be done is:
1. Interface board for pin headers - I am making an extra board to sit between the wiring and the GRBL shield. If any noise needs to be filtered out, it can be done here. It also will allow for the easy addition of software variable spindle control to be added later, as well as coolant control. If additional noise handling turns out to be required for the hard stops, it can easily be added on this board.
2. Layout and glue down of electronics - I have a board I am going to mount all the electronics and control circuity on.
3. Strain relief - I am going to put a large eye bolt into board next to the shapeoko and firmly attach the wiring to it so there is not mechanical strain on the female headers.
4. Emergency stop - I could not find a mushroom button.
Anyone is of course welcome to do any of this. Figuring out a nice way to generate G-Code would be great as well. I have been using ink scape with a plugin with very small success.