Understand that in the RE 12v system, all the electrical runs off of Battery Power. All the "magneto" does is charge the battery, and its output is not exactly powerful.
Since the constant electrical loads on the battery from incandescent lights will be higher than the magneto output when at idle, the battery actually is losing charge. Replacing the lights (headlight, pilot lights, and turn signals) with LEDs vastly reduces the load on the battery.
Removing the "always on" jumper in the casquette will allow you to turn off the headlight making the Light Switch actually FUNCTIONAL, and you can let your ride warm up without putting a drain on the battery. With the jumper installed, when you turn on the key the headlight places a considerable drain on the battery and can make it hard to start.
As for batteries, the Shorai gets excellent reviews, here and elsewhere. If you still have the factory battery I recommend getting rid of it as soon as practicable and going with one of any number of quality AGM (absorbed glass mat) or at least sealed batteries. The quality of the factory batteries is deplorable, and maintenance of them is a pain.