Hey Simon... welcome to the site! When I first got my '03 I slipped on a pair of TORs without doing anything else to the bike. I always felt it ran a bit lean after that (our bikes already run lean right from the factory) and to be honest... running too lean is not a good thing. Now I'm no expert but if logic has anything to do with it, I felt it best to rejet with something a bit bigger so I had the bike fitted with 124 mains. After that I enjoyed thousands of trouble free miles.
The following year I opened up the intake (removed snorkel, K&N filter plus bellmouth). The bike ran like crap after that because THIS particular mod threw the bike into an extreme lean condition. I was advised to either rejet with bigger mains, or return the intake to stock. I put it all back and it ran well again. This year I'll go bigger on the main jets and open up the intake again.
Hope this helps! Cheers!!