I can't see two coils going at the same time. The pickup coil and or related wiring would be the logical choice but you already changed it. ECM usually causes 1 cylinder to die and you changed it. I'd check the safeties that kill the bike. Side stand switch for corrosion and if it is water soaked. Weak side stand spring. Loose wiring to the kill switch. And also the ignition switch. Saw a number of them fail (they are repairable if you can open them up). Saw the plug in to the switch cause a similar problem. Was just about to fall off causing a make and break situation.
Good luck.
