Thanks for the replies guys. I don't know why it was tampered with. The guy I bought it from doesn't know either but it could be the original motor for the bike. I don't know much about bikes, this is my first one. I was going about changing the piston when I realised the motor in the manual was not the same as was on the bike.
I believe they changed they motor in 2005??
Here is the VIN #, maybe I'm getting it all wrong. JH9JE01A65M901183
All I can see on the motor is JE01E.
I don't think it was stolen, but maybe somebody changed the motor and wanted to hide the year?