Bit of a delayed update, work got in the way of me running more tests.
Right I stopped stripping down the machanics and reverted back to the electronics as recommended. To confirm, this issue was noticed on all 3 axis, with the Z axis being the mostr prominent.
As you have probably seen from previous posts, I have stripped back the machines electronics right down to the requirements of only the Z Axis.
As such, I have testing the Pulse + signal as per Kevins photos. Below is the results of this test. The first image is the overall signal. The second image is a zoom in on the start of the signal, wasnt sure if that was class as undesirable noise and if it would cause any issues. The third image is just the setting of the osiciscope in case I had set anything wrong.
I also ran through all the voltage pre controller again, the following is what I recorded.