That is a lot and means you have a serious noise issue.
The thing to remember is low voltage signalling (5v) which people tend to use with Mach, is that there is not much potential difference between a high and a low signal, somewhere about 2.5v and thus noise can easily cause issues. Much better to have 24v signalling but that is not so easy to accomplish with the standard breakout boards available although that is slowly changing as people realise why Industrial machines use 24v I/O.
Anyway when you are using 5v signalling you have to be particular about shielding, stepper motor wires should be shielded, all 5v signal wires should be shielded and really even power wires should be shielded. It is not enough just to have a shield, that shield has to be properly grounded and usually that means just one end and all shields should be routed to a single ground point (Star Grounding)
You may get away with just shielding your E-Stop and making sure any high voltage cables are routed as far as possible away from signalling wires.
Hood