Darcy,
Adding the sub muffler will probably increase exhaust system restriction, which can make the bike seem to run richer. If that's the case, I would suggest replacing the stock #55 slow (pilot) jet with a #52 or a #50. The Keihin part numbers for these would be N424-24-052 and N424-24-050 respectively. Robert at
http://www.motorcyclecarbs.com has them.
One test for determining proper pilot jet sizing is to adjust the air screw to 1 turn out, then start/warm up the motor and gradually turn the air screw out (CCW) at idle until the bike won't idle any faster or starts to run raggedly. Then, shut the bike off and turn the screw all the way in (CW), counting the turns. If the screw was out more than 2.5 or 3 turns, drop the pilot one size, and if less than 1.5 turns, increase the pilot one size.
Ray