Time for another update.

After a bit of a mishap while wiring up the KBIC to the BOB (note - read the manual, then read it again to ensure you understand the bit about isolated power supplies!), that led to the BOB doing strange things, then delays with post/parcels due to the snow to find out a new set of optos didn't cure the problem, and finally sending the BOB to Lester Caine (www.medw.co.uk), who discovered a fault that meant the board should never of worked in the first place, I am now finally back to where I was several months ago.
I currently have an E-stop system that works, and steppers that move via pushing some buttons on a keyboard.

Next job is to get the KBIC wired up to the BOB with it's own isolated 12V power supply, connect the spindle sensor to the Smoothstepper, tidy up the wiring, configure Mach for that lot, and then think about what else I need to do so I can make some chips.