jim almighty

I have got some Akrapovic SP cans and a K&N air filter for my 06 Fazer FZ6, just wondering if anyone could tell me if the ECU will sort out any fuel/running changes that occur from fitting one? Someone told me he had a flat spot through the rev's after fitting an aftermarket can. Also what is the best thing to do with the cat pipe? Drill it out, if anyone has done that, or buy a new one? I have purchased one in the past but it didnt fit. Any help greatly appreciated. Jim