dislike just scaling the step/mm values to make it work as it can mask more fundamental issues, and generally isn't as accurate. You should be able to measure the ballscrew pitch and work it out. The comment earlier saying the 'the Y however seemed to jerk' implies it could be stalling as the motion should be very smooth. If that is the case you need to find what's causing that, else the distance readings for that axis are meaningless.

This is pretty much what I was going to do with the gerber when the time came so how would I go about setting that up? It's belt driven via gearing rather than being a ballscrew.