Hi
Check your ignition coils with a multimeter if they have the correct Ohm measures.I had a simillar problem with yours on my MC18 and it was the ignition coils.If you dont know how to do it take a look here at this thread http://nsr250.net/forums/viewtopic.php?t=11280&highlight=ignition+coils+check+cheque
It will helps also a lot if you have access at the service manual.
Good luck