Are you able to measure the voltage between the red and black wires on the unterminated cable on the motor harness?
I have a gut feeling that the problem could be caused by a low voltage on the +5V supply.
I want to take a step back and ask anyone when the brake is pulled and I get ERROR 2 (throttle) does every display do this? If not then I am thinking the fault might be controller/wire loom. If the brake is battery ground 48volt connecting circuit and the throttle is 5volt and signal there should be no interaction except for the controller cut out.
I have a Magic Pie 4 with the earlier BAC-601 Smart Display unit and mine shows an Error 1 code (brake lever failure) every time the brakes are operated.
The brake switch simply grounds the brake signal wire when the brakes are applied, but there is also an unused +5V wire in the cable going to the brake switch.
If this unused wire accidentally touches against the brake signal switch contact it would also ground the +5V supply from the controller when the brake switch is activated:
I realise that your particular fault is not the result of a dead short circuit, but a partial short circuit on the +5V supply
could cause the reduced top speed that you are experiencing.
At the end of July last year, I had a forum member contact me via PM regarding a slow MP5, and he also experienced the Error 2 code.
He had tried a replacement throttle, but the speed was even lower than it was with the original one!
It turned out that his +5v supply from the controller dropped from ~5V to just 2.1V when the main harness and throttle were connected!
In order to achieve maximum speed, the throttle signal output needs to be ~3.25V
(or above) but the Hall sensor in the throttle was unable to produce a higher output voltage than the 2.1V it was being fed with.
He was desperate to use the bike and decided to fabricate a makeshift +5V supply
(using resistors to form a simple voltage divider circuit that would be powered by battery voltage from the lighting feed) to hopefully cure his problem.
Unfortunately, I did not hear back from him again, so I don't know whether it solved his problem, but I suspect it did.
Alan