No, the 12 minute tune will not optimize the combination of stock mufflers plus cat bypass. There is a tune (20150) which is for stock mufflers with cat box with catalyst removed which would be close - apparently it is close now that I have read the preceding post by Her3tic. Advice: get the TOR's and cat bypass. There is a stock Trumph tune and better Tuneboy ($400) tunes for it. Why worry about a legal sounding bike when there are so many noisemakers out there?