Thanks for your help we did get it working yesterday. I set it up so that home and limit- were used on each axis. Not ideally how I wanted it but workable. (I would still prefer the home to be the minimum position and not the maximum. However at least it meant that I only needed connections on the ribbon connector.
I would like to just raise another slight confusion. Setting up Mach the axis configuration refers to motor0 onwards. Your system refers to motor1 onwards. You have to keep remembering this difference when setting things up. I am sure that tidying up your documentation etc would be very helpful.
When we finished yesterday (just in time to get to the pub for dinner) my son and I had the x and z axes working. Unfortunately one of the y axis drivers malfunctioned so we couldn't finish, but at least see the light at the end of the tunnel