Steppers all working good now.

Steppers all working good now. However, trying to home I keep having issues with my limits switches. Isolated them and still not reacting right. Removed all the limit switch wires to the M1 board and found the following:

All GNDs have continuity across them, seems logical
X and X GND have continuity across them, X and Y GND have​ continuity, X and Z GND has continuity.

Thoughts?

Do you have a capacitor bridging between a GND and signal? Like 100 uF or so? There can be a lot of noise in the long wires so a cap helps filter out the noise.

Yep, capacitors fixed it for me.