Other than the tests already suggested previously, and resuggested below, there's nothing else I can think of to test, based on the information you've provided so far.
You could just try swapping out with a new identical controller, but if it's not that, then you'd need to do the other tests to find the problem.
Note that I'm asking the questions below more to get you to consider the details than to get you post them, but if you can post them it may help. It may also help you understand why it is important to think of and test each of these things, and why I recommended the specific tests I did previously.
I ask in the cases below "What exactly does "good" mean? " because it doesn't say what your test results were, it only says what your judgement of the results were. If you're very certain that you know for sure the test you did was the correct test, and the only test needed, and that the results of the test were correct, then simply posting "good" or "bad" would be enough. But if you need help from others determining if the testing was what was needed and that the results were correct, to see what else might need testing, you'd want to post the actual test performed, and the actual results of the test.
For instance, if you tested a wire for continuity, you could say that you used a multimeter on continuity setting, and tested red probe from the tip of the pin on the throttle's ground wire to the ground pad on the controller's circuit board, and got zero ohms. That could also be simply said to be "good" but the former tells us what you actually tested and how exactly it worked out, and the latter only says you tested something and judged it good.
The detailed testing info and results may not tell us anything that helps you--but it could.
Mostly it may help you learn how to test and document for yourself, if you don't already know.
Mikebate1313 said:
Hall test - halls are working
Does working mean that when connected to the controller, and the system powered on, measuring at the connector between controller and motor, that each hall signal toggles from close to 0V up to almost 5V as you manually turn the wheel?
Or does it mean something else?
Phase test - phase wires are all good
What does good mean? And which wires? the ones inside the motor, or the ones outside the motor?
Does this mean the internal motor windings are tested to not be shorted to each other, or to the stator, but that each one is the right resistance and not open-circuit?
Or does this mean that each of the wires from inside the motor all the way to the controller, including the connector, tests at zero or close to zero resistance?
Or does it mean something else?
Continuity test for throttle - good
What exactly does "good" mean?
Is that testing the throttle itself for continuity internally? (A hall throttle that has continuity is defective, internally shorted. A potentiometer throttle that has continuity is also shorted, unless your meter is giving you the resistance of each side and the center pin. In that case to know if it is good you'd need to also know what resistance it is supposed to be.)
Or is it testing the connector pins and crimps to the wires?
Or is it testing the wires from the connectors to the throttle and from the connectors to the controller and/or anywhere else they go?
Throttle is good and so is the new one
"good" means what, exactly?
Does it mean the throttles both work on another bike?
Or does it mean that they provide the correct signal voltages all the way from off to full-throttle?
Brake lever test - good lights are being illuminated when pulled
Lights where? Brake lights on the taillight? If so, are those lights powered from the controller? Or from a separate unit?
If from a separate unit, have you tested the wiring and signals from teh brake to the controller to be sure they are correct? (compared to another identical bike, or compared to what you've previously tested as correct and working on this one, or compared to a best-guess of how it should operate).
Or are they lights on a separate panel that shows what each control is doing? Or are they status lights on the controller?
Battery readings - all @13.5 v holding a good charge
Does that mean they stay at 13.5v each when under a specific known load?
Or is that when testing the bike and seeing the problem?
Or is it when just sitting there not connected to anything?
Or is it when they are on the charger at a particular point in the charging process?
When you tested for a good charge, does that mean that when you discharge-tested them for capacity (Ah or Wh) at a specific load (amps or watts) similar to what the bike uses, they came up close to their rated capacity (in Ah or Wh)?
Or does it mean something else?