ok so I think I did the ballscrew pitch check? I couldn't find a how to do video on it so went along like this, placed ruler 0'd with the drill bit, marked the bolts holding the ballscrew's, 0'd the axis and then inputted a move instruction and stopped the movement when a full rotation of the bolt came round... probably way off what you had in mind.
anyway with this I got the following results:
Y axis moved 5mm with 4.9535 on mach3
x axis moved 5mm with 5.0031
z axis moved 5mm with 3.6062
I took photos of the inside of my control box and you were right its different to the previous photos.
I found the DIP Switches were set on 3 (K3), the X Y and Z axis were also set on SW1.
there is a chart but as its in Chinese I weren't 100% sure what it meant as K3 had a 1 marked in 2 (25%) and 16 (100%)
the motors are 1.8deg
the power is apparently 220 (written on)
please see photos
I tried various settings on the motor tuning ranging from 200, 1000 at 200 to 400. 2000 at 400 I set the step pulse and dir pulse as 0 but all has similar results where there will be a clunking noise once or twice and in worse case on a few of the settings it jams.
at this point I thought could the clunking noise be down to lubrication factor?
Also I have figured out what was causing the EStop so that part is all sorted. Click image for larger version. 

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