Chris you can't hurt the controller at all thru software changes other than when updating firmware and even then it would be simple reload.

So what I think may have happened is you've maybe damaged the Mach3 Xml file or Cslabs plug-in. But to be honest I'm struggling to fully under stand what you did so can you be more clear.!

Worst case scenario is that you'll need to re-install Mach3 and all the Cslabs plug-in's and re-enter your settings.
The V2 MPG Encoder doesn't need any setting up it's all done for you, just make sure you terminate the Canbus with the provided terminator.

But given the problems you seem to be having can I make a suggestion that you slow down with adding things like MPG and just get a sound basic working machine. Then start adding extra's like MPG because sounds to me like Your trying to run before you can walk.!!

Why your having these problems I don't know because normaly provided you read the manual and understand the different way they use pin / Channel/enable setup compared to mach default way then these controllers just work and don't give any troubles. If there are any issues it's always just a simple setting that needs changing.

To reverse an Axis goto Config / Homing & Limits and use the Reverse option.

Give me clearer details on what you did and I'll try to make sense of it for you.!