I had a similar problem. but i am goood now. To much fuel/oil was entering the engine and it was not all burning off... I did the topend change out as well with a piston to boot.
Check the Spark plug gap... it will foul if the gap is to big...
If the plug is fine, check to make sure the bike is putting out enough spark through your electrical system. Check ur spark... if it is blue, ur good, yellow bad.
Plug 7 is hotter, use it when ur breaking in ur bike and when ur in colder weather or driving at slwer speeds.
Plug 8 is medium use...
Plug 9 is colder for high speed/heat enviroment. (based on the book i read)
Fuel oil mix: I changed mine from 32:1 to 70:1 when I switch to a high quality racing oil. I spend most of mine time at low speed climing mountains.
Check your carb out and make sure ur choke is full off when warmed up and riding. Check the Air inlet screw... is it set to far open/closed?
Hope this helps