Hi Tawapah,
After carefully studying your photos, I don't think that the scraped insulation on those windings is severe enough to be causing a problem, as none of the exposed sections of the copper windings appear to be touching against other exposed sections.
I observed much worse physical damage to the armature windings on my vacuum cleaner motor after one of the bearings had completely failed:
The vacuum cleaner motor has been working perfectly since I carried out the repair at least two months ago. In addition to replacing both of the bearings, the windings had to be separated, soldered, painted
(to insulate the exposed wires) and then super-glued to keep everything securely in place at high motor rpm.
Assuming that the wheel still turns normally by hand, can you feel any noticeable resistance if you turn the wheel slowly and then gradually apply a small amount of throttle?
When the "click" occurs, does it affect the Battery Gauge LEDs on the throttle?
I suggest that you start by removing the controller from its housing to see if the LED on the back of the controller is producing an error code
(regular number of flashes).
Also check that the Hall sensor connector is properly connected.
If the controller does not identify any faults you should see just a single flash when the controller is initially powered up and then nothing else.
If there is a problem with the Phase windings, I would expect to see seven regular flashes continually being repeated with an obvious pause in between.
A problem with the Hall sensors should produce five regular flashes. However, five flashes will also occur if the controller is powered up with the stator removed from within the motor's magnet ring.
If you do not see any error codes, you can turn Off the battery power and then disconnect the three Phase wires from the back of the controller
(making a note of the positions of the Yellow, Green and Blue wires before disconnecting them).
With the three Phase wires disconnected, use a multimeter to measure the resistance between each pair of Phase wires
(Yellow and Blue, Blue and Green and Green and Yellow) to see if there is any noticeable difference in the three readings.
Also use a multimeter to check for continuity
(very low resistance) between the Phase wires and the metal part of the stator to determine if any of the windings are shorting against the metal.
The Phase windings should be electrically insulated from the metal stator assembly that they are wound around, so you should not be able to measure any continuity between the windings and the metal parts of the stator.
Unfortunately, it is difficult to know what might be causing the problem without knowing exactly what was done during the bearing replacement at the local metal shop.
If the controller was removed, perhaps the Phase wires could have been inadvertently mixed up when they were refitted.
Hopefully, removing the controller will enable an error code to be seen or perhaps an obvious problem will be noticed with the wiring inside the controller housing.
Alan 
