Please remove
Coils? Have you checked for spark once it stops running and you can't fire it back up? Rectifier connections good? Usually these are burned up. Another thing would be check the fuel and ignition relays. I replaced mine after the bike bogged and died on a ride. Never experienced any issues prior. It would start and run sometimes after that. The relays were shot when I tested.
Hope that helps
A fuel injected bike needs a healthy battery and charging system to operate correctly. At lower engine speeds you need enough amperage to run the fuel pump, computer and lights. You might want to check the charging system too. It is also possible you had high resistance in a battery connection that was corrected when you changed the battery. Since the fuel pump relay was being tortured you might want to consider replacing it.
A shorted battery is a shorted battery. Coils are not a major current draw compared to the fuel pump and computer.