Thanks for that info, the meter displays the throttle works by twinkling the LED according to how much voltage is going through it so it seems to be fine, my MM read the right voltages when used or not too. As for the other 'extra' wires, there's only 4 if my memory serves me correctly, 2 are possibly for the brakes, 1 is the PAS which is the 3 wire 1 and then there's the learning wire too, the rest are all filed with the basics to get the ebike running as it were. As far as i'm aware there is no alarm although 1 of those 2 wire ones I think are for the brakes could be, they both have 2 wires and the same colour too and both measure 5V. The battery wasn't fully charged but was around 3 quarters roughly and the hall sensor wires you mentioned were already checked and tested fine, both motor & controller side and phase wires only work on the motor side as mentioned previous.
Is there anything specific inside the controller that controls the phase wire pulses that might be at fault? I'm intending on opening it up anyway so any ideas/suggestions where and what to look at are welcome.