I had a lot of issues with my '05 last year. I replaced the spark plugs, plug wires (mine were cracked through!), primary TPS, the fuel filter and still had issues. I also disconnected my PowerCommander and tried to use TuneECU with different tunes, but couldn't get it to run right. I took it to my local dealer and they replaced the rubber gromets that hold the throttle bodies to the head but it still ran like crap.. I didn't have time to mess with it anymore.. so I took it to the Austin dealer.. They went through everything, inluding installing a new battery and another new fuel filter.
The Austin dealer discovered that the my local dealer had not tightened the throttle body gromets and I had huge vacuum leaks! They tightened everything up. I had then loaded TORs tune since that's what my PowerCommander map was based off of... and low and behold the bike has run great ever since!
My bike does have a lot of miles on it (70K this weekend) Basically it was a combination of plug wires, rubber throttle bodie gromets, and getting the right tune back in there...