Testing revealed two problems. Firstly, the y-axis kept stalling. Issuing the nudge controls to travel almost the full length of the axis would result in the gantry moving at speed and then stopping suddenly while the motors made a horrible wine. I Inspected the y-axis and found that I still had one of the old worm type motor couplers attached which was wobbling like crazy. I needed a new one but didn’t want the slow boat from China to hold me up. I temporary fixed the issue by mounting the motor on some acrylic and attaching this loosely to the side of the machine. This allowed it to move (dance!) freely re-leaving the friction on the lead-screw.
Secondly, I had a lot of noise, not just any noise but terrible vibrating squeeing noise especially when the X-axis slows to a stop I checked all bolts to make sure everything was tight but to no effect. Later that night I did some research, again what I was witnessing seemed to be quite a common problem with CNC enthusiasts. There were many reasons ranging from oil pumps to bearings dying but the most interesting was in the subject area of mechanical resonance where the stepper motor(s) starts to get in-sync with the natural frequency of vibration of a component such as the lead-screw causing noise and vibration. This could lead to unnecessary wear and loss in accuracy (reason why the machine is quieter at high speeds than lower as the change is frequency). This is probably the reason that my original x-axis uprights didn’t have a problem as the supports were built with MDF which would of absorbed the resonance from the stepper motors.
A useful link that may help me in the future is this one by a enthusiasts with the same issue:
I will carry on and try to fix the issue at a later date. I still had some configuration that I want to do first which could affect the speed the machine will be running which in turn will affect the resonance.