I had bought (1.5 years ago) a 2006 that had sat for a number of years. I replaced the throttlebody, and changed out the fuel in the lower tank and a new battery. When it wouldn't start, I shot some starter fluid down the throttlebodies and it finally started after a couple of tries. That bike has since been sitting out in a shed and and I have gone out and restarted several times with no issues.
My suggestion would be to drain the main tank as indicated below (see yellow circle - that tube goes down to the bottom of the lower tank and will drain just about all of both tanks - having enough gas cans on hand to hold both gas tanks):
Remove the upper gas tank, and the air filter housing to expose the throttle body tubes.
You can try shooting some starter fluid down the throats of the tubes, or remove the tubes and expose the throttlebody.
Just a suggestion, nothing I haven't already done.
Would help to hear from the fuel pump before getting into any of this good stuff.