03 fs650 bad missfire

hello all, newbie to the site
recently bought a 2003 fs650e as a non runner due to bad stator, stator was replaced with a rewound unit and the bike fired right up and ran great for around 3 hours use.
The next morning i got the bike out, fired her up and went on my way, after around 10mins of riding i noticed a little missfire as i changed gear and got back on the throttle, didnt notice it again for a few miles untill i stopped at a set of traffic lights, as i came to a stop the bike cut out, pushed her to the side of the road and after a good 20-30 kicks she ran again but very lumpy, as i pulled off the bike just missfired/backfired massivly and trys its best to cut out as soon as the throttle is touched, its REALLY bad and the bike is just un-ridable,eventually it just cut out again, tried kicking it back up but soon gave up after a kick back left me in agony :cry:
So after a 2mile push home i went over the basics, carb off, cleaned it out, all connections checked(all ok), new plug(no differance), stator removed and sent back to be tested(stator fine), valve clearances were all set and adjusted to the proper spec.
Really not sure now where to start with this missfire so any information/ past experiances of a simular problem would be much apriciated.
Thanks

just checked valve springs, all still in 1 peice and clearences are still all ok,
one thing i forgot to mention is that as soon as i got the bike home the first thing i did was take out the stator to check for and dirt/water, i gave flywheel and stator a good clean with some wd40, re-fitted and fired right up, a quick spin down the road and all was well and i thought it was fixed, parked it up and put the tools away thinking job done, jumped back on the bike and as soon as i touched the throttle the problem was there again :angry: