You might try testing just certain parts of your program to make sure that you have the electronics working. I don't know which shield you have, but it probably has example code for it which you can use to test and see if you have the wiring correct. From there you can then try and get it to work with the Sun Harvester Program.
Which code and which shield are you using? Knowing might help me understand better. Also, are you using the latest version of the program? I'm assuming that you are doing the electronics yourself?
The limit switch isn't really meant to protect anything. In this case the limit switch is used as a homing switch, and if it is triggered anytime after the machine resets, it will not stop the machine. Both the altitude and azimuth pins should be set as the same by default although they can be separate if needed.
I'm not sure I understand the question but the switch is just a basic switch, so I'm sure you can find one easily. The switch is technically wired the same as a button if that helps. Is that what you are asking?