yamaha motor runs fine on trailer but boggs down in water

I have a 2004 yamaha 250 HPDI that when the boat is on tailer it runs fine. You can keep it running on trailer for long period of time and continue to give it gas and it still runs perfect. However, once you put in water and give it gas the motor acts like it stops getting gas or it seems to bog down. Sometimes you can ease down the throttle at low rpm and it might be fine for a very short period and then it stops. It sounds like the motor bogging down. I have checked the pressure in the fuel line and it checks out. I have ruled out bad gas. The fuel filter has been cleaned/replaced. HELP

It sounds like it is time to replace all the fuel filters including the one between the VST and the high pressure pump.

How many fuel filters are there? I have replaced the fuel filter that is visible on the side of motor. Where is the filter that is between vst and high pressure pump. Do you think this problem has anything to do with a throttle body problem? I purchased this motor last summer and the first time I ran it it bogged down to point I could only get it to idle. This next morning when the motor was cold it ran for about 10 min. At about 2000rpm and then it bogged down to only idle. From that point forward I've only got it to idle or run at the lostest rpm(barely in gear). However when its in the water I can put it in neutral and rev it up with no problem just like if it was on the trailer. Your thoughts????

There is probably a filter mounted in the boat somewhere. There is a screen inside the VST and the little filter on the fuel line between the VST and the high pressure pump. The little filter I am talking about is around $105.00.

Sorry to ask such a basic question but where is the VST and what am I looking for to identify the high pressure pump. Is the filter and screen you are talking about located on the boat. Does this filter look like a oil filter. Looking back at some invoices i believe this filter was replaced(but the invoice only says it cost around $12, could this be an oil filter and not fuel filter?) but the screen you are talking about has not been replaced or cleaned. How big is this filter you are talking about Your theory is making sense because the boat sat for about four years without running it before I put this motor on the boat.

You are going to need a service manual for this engine if you are going to do this service your self.