2005 225 xxl rough running at power reduction

[Pctim]

I have a 2005, maybe 2004 Mercury 4 stroke 225. I think it is the one that Yamaha made for Mercury. Twice now after fishing most of the day and running well at various power settings, the motor runs rough when I reduce the power from cruise. The engine runs very rough, sputters coughs but then smooths out after a few moments. Then I reduce power again and the same thing happens. Not exactly what you want to hear when you are 20 miles off shore. I replaced the fuel, thinking it was fuel separation, which I do think had happened. Has anyone experienced this? The motor has about 1000 hours on it. Are the other filters or whatever that may be clogged? Timing or throttle issue? I am at a loss and think my mechanic is too. HELP!!!