Hi Darren,
Not sure what you mean by "tried inverting the signs on both the input and output channels". Inverting the InputGain0 and OutputGain should reverse the axis.
Regarding Limit Switches it sounds like you need to reverse the polarity setting for the limits. Change the "Stop when low" setting to the opposite state you currently have it to see if that helps.
When the Axes are Slaved then a Limit Fault on either axis should disabled both the Master and the Slave. So you shouldn't normally need to do anything.
Regards
TK