You do not need to enable anything in Mach related to MPG, the CSMIO will do it all as it works interdependently of Mach thus the much better motion/precision. Enabling settings in Mach that are not needed may actually make things worse as they conflict with the plugin, a classic example of this is enabling the Index in Ports and pins when you are using the Encoder module.
The E-Stop on your machine (not the pendant) I think needs to be wired into your E-Stop string on the Machine, ie you connect the E-Stop chain of your machine through the contacts on the MPG Module that are beside the power connections. The E-Stop on the handheld pendant basically works a relay in the MPG Module, this is so that you are not relying on the Canbus for relaying your E-Stop signal.
Hood