2003 Yamaha 115hp 4-stroke - shacking issue

[Reeltoreef]

Make this short and sweet! 2003 yamaha 115hp 4-stroke with 2553 hours....has been a fantastic motor! Recently found a hatch leaking water on top the fuel tank and water and years junk in fuel compartment did compromise the tank. I pulled the deck and dropped in brand new tank, new fuel lines, new Perko gas cap/vent(Same as before), and did new fuel/water filters and 100-hour service. THE ISSUE is that engine runs great for hours or within the first hour then all sudden shacks/lose of power for like 1-2 seconds at 4500rpm's and over and then keeps on going and or also when throttling down occasionally will shack or hick ups a second or two before dropping it into neutral. This is the same issue issue happening when I had water and junk in my old fuel tank even after draining the tank and replacing new fuel/water filters after every time running the boat. I know this issue may be a little issue considering the hours on the engine but could I have damaged the fuel injection system or something else when the original issue of water getting into the fuel lines back a few months ago?? Any feedback is greatly appreciated!!

 

[99yam40]

If you had water getting to the motor, yes it needs the whole fuel system on the motor cleaned, not just the filter changed