Those symptoms sound very much like the precursor to pump failure? I've had a few submersible fuel pumps go on cars and bikes (not the XT mind) and they've all squealed or got noisier just before they conked out. Any trapped air will usually clear itself very quickly in a pressurised fuel pump/system. Sorry, I don't mean to sound like an angel of doom!
If it is the pump and it does eventually give up the ghost, then whatever you do, don't look at the Yamaha genuine part prices - you'll have a heart attack! They only sell the complete assembly (pump, housing, sender etc.) All is not lost though... If you take the assembly out of the tank and open the casing you can just replace the pump unit. The pump itself can be bought from various sellers on ebay (and elsewhere) for around �30-�35.