I recently encountered this exact issue on an IGM-4NC running the Fanuc 15T-a control.
I do not have schematics handy for this exact model but should be similar. Inside electrical cabinet, Look for the setup module with (2) relays per axis. These are typically labeled -Z/ +Z, -X/ +X, etc. This board is responsible for carrying the E-stop string & the N/C stroke limit switch circuits to the Fanuc I/O units giving the all clear to run. In my experience, If this board is damaged or shorted you will get over travel alarms in all axis.
Secondly, one or more of the Fanuc I/O units may be in a failed state. I have also come across this in similar instances.
Have you experienced any power failures, brown-outs or backup battery failure?