I wrote a little G-Code program with some help from the Machinekit documentation so I can run some tests that will help me with this tuning. The main thing I am worried about at the moment is loosing steps because of incorrect speeds or acceleration. To test this I am going to set up a program that will cycle for about 10min or so just making movements in one axis to see if it drops any steps. If I note it's position when it starts and compare that to the position it returns to then I will know if it has lost any steps.
This is a video of running this program. It is using a feedrate of 100mm/min which the motors seem to like. So this should be a good starting point that I can improve on.
I'm thinking about different ways I can share the programs between different computers. I am probably going to set up a Github or similar account that I can store the machine definitions in. Then if the SD card this is running from dies I still have the configurations and they can easily be transferred to other machines or shared.
For the G-Code programs I am probably going to set up a Resilio Sync installation on the controller. This way if I want to edit the files on a different, faster computer I can. Then once I'm finished editing the files it will be quite quick to move across to the controller.