I have a 2004 yamaha 250 HPDI that when the boat is on tailer and 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 check the pressure in the fuel line and it check out. I have ruled out bad gas. The fuel filter has been cleaned/replaced.
