After swapping ECMs, a TPS reset should be performed because the "reset" value is stored in the ECM and is specific to each bike. Since the TPS wasn't also swapped between bikes, the stored value must be reset.
You shouldn't have any compatibility issues, but you might want to check the code.
Do you mean you plugged in the exhaust actuator electrical connector, or the metal cable that runs down to the muffler, or both?-Fired up the 06 (added the exhaust valve cable to the bike) and the check engine light came on. Ran rough, but got it to 1100 RPM with the adjuster.