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I'd check my battery and ground connections. I know my ECU is fussy about having stable voltage, and a poor or high resistance connection can create a reference voltage that jumps around as the bike vibrates. Try bypassing the ground strap with a second wire. Use an analog (with the needle, not digital) meter to monitor the voltage to the ECU as you fiddle with the connections, especially any that might have been stressed when you pulled the old battery.
 
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