It is not going to be a construction issue, slight differences in amount of copper will go unnoticed.
This will be a connection issue, either in the connection of the coils in a phase ( a reversed coil will knock 2 coils out), or one phase is 180deg reversed at the star point.
Yes it will make power and under light load will behave as a single phase machine with all the disadvantages.
If you load it down hard it will work better than a single phase winding as the low voltage phase will conduct when the IR drop of the better ones exceeds the battery voltage. For mppt you should never load it that hard and you will be effectively reduced to single phase.
A fundamental first test should be to short all 3 leads and turn it, then compare it with 2 leads shorted. The lumpy single phase resistance to turning shows immediately. That and a voltage test on one phase should be good enough but checking all 3 phase voltages is a wise move.
Use the rectifier to determine cut in speed, measuring dc volts, again short after the rectifier and if you get lumpy torque and the machine is ok directly shorted then you have a diode problem.
Flux