HI Ozz!
Is it a stolen/ recovered at some point in its previous life? If so, it's possible that the VIN may have been partly ground away by the thief before the police got to it and has had to have been restamped on it. Some years ago I bought a stolen/ recovered KMX125 via a police auction that needed the number stamping on again. It was a new bike so didn't need an MOT but I sold it to a dealer with no problem. Maybe you can talk to your local friendly MOT man and see if he'd be happy to do it on production of the V5 at the time of the MOT. If you are struck on having the bike I would strongly suggest you wait until the V5 appears......
Alternatively, I'm sure there are plenty of other CBRs about if you can do without the a**e factor if you decide to move it on at a later stage.
Regards,
Gary.