Ebike going up a hill controller and motor gets hot causing a circuit break
As one commenter suggested, the issue is likely not that the voltage is incorrect, as a 36V battery means 10 typical Li-Ion cells in series, which will have a fully charged voltage of 42V.
It is possible that your battery pack had a BMS or some kind of current limiter or fuse system that prevented too much current from being drawn, or that some of the motor controller settings, such as current limiting were changed.
It is also possible that when you modified the battery pack you used a different type of 18650 cell that those originally present in the pack, or used a different type of conductor to add those cells to the pack, which has a different amount of resistance.
To debug I would first suggest using a current and voltage meter to measure the power output and current draw to ensure that your usage is below 350W, and then possibly adjusting the settings on your motor controller.