Well - first off I'd change that kill switch out with something that works lol, the stock ones are known to be junk - that alone will cause you trouble.
Once you get a new & better switch - you may find it was the source of your probs, others have found this to be the case with theirs.
You can also bypass the switch entirely and use the choke to shut down, just to diagnose if the switch is indeed messin' with you - once you've eliminated the kill switch problem, get back to us with how yer bike is doin'
Good luck man, hope that's all it is!