I had another idea to offer up for comment or someone's early trial. Thi is about the battery switch location and the need to toggle it at times to wake up the controller. What the controller really needs to see is no voltage for a while, the return of voltage wakes it.
Idea: place a normally closed, high current relay between the center of the switch and the controller. Place an instantaneous, push button control switch on the handle bars. When the controller needs awakening touch the push button. The relay opens. The controller sense the return of voltage and wakes up.
Worth a shot??