If you replace your plugs, make sure that they are genuine. There are a lot of fake spark plugs out there and misfires is typical of faults with them. I had a Honda 750 bike with dodgy NGK plugs in it which took ages to fathom. I found pics on t'interweb of fake plugs and mine were. A good set from a reputable supplier and the misfire was gone!
https://www.google.com/search?q=fake...=1920&bih=1064