Hello Sol, the VIN of the bike is burned into the ECM of each bike, and the SERT is married to that specific VIN when its first initialized. As stated before, the SERT is married to that VIN number in the ECM.
While you can get a replacement ECM from a dealer I doubt they will burn, or program, a different VIN number into the ECM just so you can continue to use the SERT.
Also, do not plan to swap the ECMs of the 03 and 06 bikes. They changed the ECM in 05 to prepare for closed loop operation, so the ECMs cannot be swapped and made to work, as I have read. I havent tried it though.
I think your only solution is to buy a new tuner. Be careful if buying a SE product. MoCo makes the Street Tuner, and Pro Tuner. Only a dealer can use Street Tuner, and only to download a map. You will require a Pro Tuner if you want to tune the bike yourself (Smart Tune), or if you want the dealer/indy to dyno tune the bike. The Street Tuner just allows the dealer to easily load canned maps to the bike, and is not worth the money for most riders, IMO.
You might also consider a TTS-Mastertune tuner. They made the old SERT product, and have improved on it since MoCo dropped them in 08.
HTH
Dennis