I have a curious phenomena on my fuel pump which might help. I have absolutely no reliability problems so I do think it's OK.
When I've stripped parts of the fuel line, emptied out fuel and put it all back together, the fuel pump 'burps' but sometimes doesn't make its sustained 2-3 second whirring noise when the key is turned on, which is the pump pressurising the fuel rail. It must do that.
If I remove each QD and poke the valves to release some fuel and back pressure, then reconnect, the normal pump sound returns when the key is turned and everything is fine.
I suspect you can get an airlock and the pump locks out with some kind of over pressure sensor. It's not uncommon either to find the fuel filter disconnected (wrong hose clips used) inside the tank. If you can get pressurised fuel from the delivery side of the QD, the filter should be OK.
You're throwing in other issues to do with the brakes which aren't going to stop the bike starting. If it has a good battery yours may still be suspect, try a car battery, get the polarity right!). ECU 'reset' isn't an issue to affect starting either. If there's fuel, compression, and spark at the right time it should run. However, these bikes can get flooded easily if you've been cranking on a low battery (impending doom for the starter relay - now you've read about it!). Either remove the plugs, dry them out, heat them up on a stove or gas torch and put them back hot. You shouldn't be twisting the throttle either when cranking. Just leave it at idle and crank 'till it starts. The ECU is in control for starting not your wrist and idle is 1100rpm!
These bikes depend on the battery for everything. A green light on a tender doesn't mean you have a good battery capable of putting lots of amps into the starter when you need them. When these motors get flooded after too many starting attempts, they often fire up next day when dried out. If I have to crank mine more than 3 or 4 times that's unusual I stop and wait a few minutes before trying again.
You mentioned the kill switch which must be 'off' mid position for starting, there's also the sidestand, gearshift and clutch interlock to think about. If you pull out a plug and get a spark then these are all set hot to go and there isn't a problem.
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