The only things I need to know are the volts after charging and the watts from the throttle, so we have 36. 1v and 150w, right? The watts is important, so be clear about it.
You charge the battery off the bike, so it can't be anything to do with the charger. That must mean that some battery function must be switched off by not having something from the controller because of the lack of comms.
We had a few examples of guys with these bikes where the battery voltage would stay low even after replacing batteries and chargers. Maybe this confirms that the controller might have some influence on it. On the other hand, other guys have done this conversion without problems, though there are different battery versions because some have two extra wires, like yours, and some have three.
I don't know what to suggest now. Your 150w rules out a false motor connection sequence. If it were my bike, I'd be stripping down the battery to figure out why you only have 36v instead of 42. It's like your battery is half switched off. The charger and battery don't know anything about the changes you made, so it must still be charging to 42v. That's what I'd want to check first. Unfortunately, without the comms enabled, you can't measure anything from outside the battery.
Where do you live?