What specifically does it do when it doesn't re-start? Cranks fast and not fire? Fires up and stumbles? Cranks slow?
You may be getting the system voltage error just because the bike is having a hard time starting.
With the race ECM in have you tried to slightly open the throttle while cranking on restart? If you are shutting it off cold it is still very rich. Opening the throttle blades will give it a little air to compensate.