Sounds like you've done a very comprehensive diagnostic on your bike. For all the time and money spent, seems like it may an issue for the Honda dealer.
They can plug into the ECU and hopefully get a fault code to lead to the problem.
I assume the battery is STRONG! ?? Not just showing 12 Volts, but truly strong.
I know you checked all the safety cut out switches and kill switch ... but my advice is ... CHECK THEM AGAIN! (Clutch, side stand, kill)
So many times turns out to be a corroded contact point, loose connection or something silly like that.
Before spending the big money on a new ECU ... I would have let the Honda boys have a go. I assume your bike is OFF warranty? ... but in some cases Honda may do a "Good Will" repair for Free. Not often, but has happened if it's something odd.
I have no brilliant ideas beyond the rambling above. All the best!
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