1. your first set of plugs could be bad due to age
2. Your second set of plugs could just be bad period (not unheard of to get bad plugs new out of box)
3. Check your air filter...if something isn't right it might be blocking air into the intake which might cause the bike to run rich. If running a K&N is it over oiled?
4. What pipes are you running? And have you check your exhaust gaskets
5. Try the battery trick just to be sure.
6. Have you checked your O2 sensor? They do go out ocassionally. There are checks for them online and if I recall all you'd need to do is disconnect it from under the seat and use a standard voltage meter to check the resistance.
7. Double check your wires under the tank. Its fairly easy to pinch and damage those wires as well as the little hose under there.
8. Check for damaged wires at or near your ECU under the seat. Unlikely but it can happen.
Last, and this is just a remote possiblity...look inside the bottom of your air box...is it thick (dripping thick) with oil? if anything more than a film of oil is in there you could be pushing oil out the Crank case vent at the top of the rear cylinder and into the intake. Normal amounts aren't a big deal but if you had bad rings, it could push a ton of oil out and gum up your carbs. Simple check is to check if your oil is low and double check the airbox when you change the filter.