Managed to fix it! Turned out it was the steppers overheating! adjusted the pots, and eventually got it going! However, the head is only moving half as much as it supposed to, it appears that all axis is coming out half scale!
Having thought about it for a bit longer, i realised it wasn't just that they were overheating! So i had two different types of drivers for the motors, one was the A4988 and the others were the upgraded DRV8825. Both have different micro stepping, 1/16 vs 1/32, hence why one axis was moving more than the other! After accidentally blowing up the A4988 i replaced it with a DRV8825, which corrected the issue! I then had to correct the steps per mm for the new micro stepping.