I am trying to run 3 motors for the z axis, however is there a way to have 3 individual endstops that will stop each motor once the corresponding endstop is triggered?
That is something the firmware must support. In case you just choosed wrong category, Repetier-Firmware V1 supports this only for 2 axis. V2 firmware supports this. But on both you can use motorised bed leveling to make all 3 axis at same level with G32, which you would do when you think they are out of sync.
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