Keeping your Stock ECM with the bike - Load your stock EEPROM (after saving for safety) in one ECMSpy window - Open the Race EEPROM in another seperate ECMSpy window - Change Map values and other settings on your Stock EEPROM manually so it matches the Race EEPROM, - Rename, Save, & Burn back to bike.
Your just using the opened Race EEPROM for a reference to make the changes to your Stock EEPROM. The ECM won't know the difference this way since it keeps it's original Firmware.
The ECM is just a platform, as long as the same firmware is used when burning back (regardless of modifications made to it), you should be golden.
Hopefully Octo or Gator will confirm/correct the steps above if need be.