Hi Peter,
Great news that you have your machine working

Looking at your .xml, you still need to correct your Port & Pin allocations which are wrong otherwise Mach3 will get confused and you will have inaccurate results and problems in the future.
The Digitize light is controlled by the Input Signal
Probe.
With regard to Motor Tuning, this is basically done by ‘trial and error’; Ideally Acceleration should be set to the highest value that works with 100% reliability even if it means reducing Velocity slightly.
CNC is a long road and I have been on it for more than 20 years now and still learn something new every day. Keep at it my friend.
Tweakie.