Try taking it to your local locksmith for re-keying or have him duplicate the keys.
It ain't cheap, but remember that your helmet lock and fuel cap use the same key. It's probably cheaper than replacing all of those or the damage you'll have to do to remove them to replace them. The helmet lock needs to be unlocked to remove it from the frame. That requires an ignition key. Same for the fuel cap.
Yamaha does sell key blanks, but they're outrageously priced. Last and only one I bought cost something like $25 IIRC. I'm sure not all locksmiths will have them but my local locksmith had the same blank for 3 bucks when it was all said and done.