Oliver
I don’t think you need to go to the trouble of writing your own CNC control software. There are several CNC control programs that are being used by thousands of CNC users around the world. Three of the very popular ones for hobby and small business users are. 1 LinuxCNC free 2 Mach3 around $170.00 3 Mach4 around $200.00. You will need to change from the arduino, GRBl electronics and stepper driver to a older computer that has a parallel port. Then you will need a Break out board the attaches to the parallel port. Then new stepper drivers that are fed info from the computer via the BOB. There are Break out boards and stepper drivers that are low cost and you can get high end units that can cost as much as you have in you whole machine.
All of these control programs handle homing or reference switches and full limit switches without problem. With full limit switches enabled it is impossible to destroy a switch because the control software will stop the axis before that can happen.
If you would care to there are a group of us that gather on Saturday evenings at 6 pm PDT here. Google+ Hangout Live tonight at 6pm PST
We talk about a lot of subjects and you are more than welcome to join in.
Hope this helps
Dave