You will probably have to lean the bike down a little for the less restrictive exhaust. If turning in the mixture screw 1/2 turn at a time doesn't do it, you may have to go with a smaller pilot jet. The spark plug condition will speak more truth much quicker to you than the exhaust pipe.
If you find that you have to turn the screw in less than 1 full turn out to lean it down properly, you need a smaller pilot jet. To check main jet mixture, run at your fastest highway speed feasable for 15 minutes,hit the kill switch as you pull in the clutch....don't let the engine turn over... then check the plug. This will give you the sure fire truth about your high speed mixture. Change your primary main jet first... it sees more action than your secondary main, which is only functioning at higher throttle openings.
It is hard to accurately diagnose an engine from 3000 miles away, some rules always apply, and if I had to guess I would bet you need a smaller pilot jet and some low speed screw experimentation. Plug checks are the most accurate way, and I also recommend an iridium spark plug, especially for singles...hotter spark, and they last forever. Good Luck.
