My 2004 FX HO which used to go 58-59mph now only goes 45-50mph. The oil level reads full @ about 3qts and was recently changed. It had been about 1yr since I last operated the waverunner but I stabilized the gas and stored it in the garage. What might be the problem?

i suggest you fill it with fresh gas and check the oil level might be too high.

Check for a fouled plug

sounds like the oil in filter problem that is well know with these skis
after an oil change if too much oil is put back in it will be sucked into the airbox and clog the air filter resulting in a loss of top end performance

try removing the air filter and running the ski
to see if the performance returns, if it does replace the filter and remove some oil till it is between half and full on the dip stick

kev