Originally Posted by Buckster
Could be the carb breather pipe getting pinched under the seat.
I second the Buckster's emotion - did you check the "evaporative emissions control" hardware? You didn't state that you have either checked or removed it.
From memory a few have had a similar issue and found it to be a pinched line. I don't know much about the fancy SAS system (sic?) on the 04- bikes but folks have been removing them in order to get the engine breathing properly and reliably.