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I have a friend's 03 STX 900.
As far as I know it has had the same symptoms since the middle of last year.
After riding for 20 minutes- 1hr, wide open or slow, time may vary, it looses power. The 1st time I noticed this I had wide open throttle and it dropped to 6K rpm's for a brief second then jumped back to wide open throttle(around 8K I think but don't remember). However the longer it is operated the more power it will loose, after riding it for 30-45 minutes as fast as it allows it will only go 2-3K RPM's. As it looses power you have to adjust the throttle back to keep it from surging. After it sits not running for 20-30 minutes it will run fine.

Last year my buddy installed an electric fuel pump and replaced all 3 coils to correct this problem with no results.

Any Ideas what the problem could be or what I could do to diagnose the problem?
It seems to be related to it heating up but sometime it will run an hour sometimes only 10 minutes before it acts up.
 
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