Four years ago I got my ECU done by Ivan's. He told me then that it didn't matter if I kept my Fi2000 fuel tuner on, but that I should take it off as it would run better. I was very happy with how it all ran after the ECU flash, and kept it on. Bike wouldn't start a couple of times recently and...
Autocheck: motor warning light on or any fault code in the display?.
Before replacing anything is useful to professional check the charge circuit: from alternator to the regulator output to see if it really is charging the battery.