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Well motors will try to "ground" through some other pins. That may be the reason why you don't have 5V on Fault pin for eg. It's going to burn your electronics sooner or later ...
Mictostepping pins shall not be an issue. They are either not connected or, giving 5V signal to driver. If jumpers installed on MS0, MS1 and MS2 pin you will get short with 5V pin on RAMPS.