There were many published issues with the '04 225 4s Yamaha. My two were no exception. After years of frustration and spending thousands of dollars to fix problems, including what you are encountering, I gave up the ghost and purchased a new Yamaha 250 4s. My suggestion would be is to bite the bullet and get the engines into a reputable Yamaha service center and have them take a very close look at them. Even then, after hooking them up to their computers to isolate the probllem and paying for a fix, the engines could raise their ugly heads at any time. I'm a licensed Captain and couldn't afford to an operate engine I couldn't depend on. Your engines may not be included in the batch of problem 2004's. However, I'm smelling a similar rat based on issues you're having that mirrored mine. Get it to a certified Yamaha Mechanic and best of luck from there.
Check the fuel line to be sure it’s not partially pinched or the fuel line isn’t collapsing inside due to ethanol fuel. I have had this problem before with pinched fuel line. Would run good then start starving for fuel. The line was kinked in the bilge area. Also check Your thru hull gas vent. If the screen is clogged with salt deposits , it won’t vent properly and create too much pressure inside tank for fuel pump to over come at higher demands
But did you look at the plugs when you pulled them out? Were any of the plugs bright grayish white, dark black or even wet? It sounds like you may have an ignition coil that is going or went bad and you're running a cylinder down. You may not notice it at lower power settings because all of the mass is still spinning. When you try to get to 225 hp you're only getting 169 hp which will only spin the prop 4000-4500 RPM.
