had this same thing happen to a stock bike of mine!! Odds are it is the stator going south on you... it will start of popping missing, cutting in n out, then before you know it no spark at all, period no mattter what you do.. my recommendation to you is get a new stator (oem), also not sure how much oil you have in the pipes but if your getting alot of smoke out one cylinder and lots of oil i would suggest changing your crank seals... you do not have to remove the top end if you are good, just split cases and with crankshaft fixed to upper case, and give yourself enough room to install new crank seals,... start with stator, if not change crank seals, just my .02 worth