I spent some time writing a long blog post about some testing and configuration, and then realised it was almost a set of instructions. I re-wrote a few lines and posted it on the RepRap Builder's Wiki, in case it was useful for anyone else. You can find it here:
and a couple of pages here:
Basically, I've configured the X, Y and Z axis, so that if you tell them to move 10mm they move 10mm.
I did find that the x-axis stepper was slipping, as the x-axis wasn't consistent. I disassembled the stepper and took off the grub screw. I filed a larger flat on the shaft of the stepper, and re-assembled, making sure the grub was tight on the flat. It moves much better now.
I have just started to test the extruder... more soon.