one day runs great the next sucks

i have an 05 f-60 with jet drive. ill be out all morning runing up and down the river and no problem. on my way back ill be on step and my engine starts to shutter. i found a vacum like off my fuel pump i reintalled that got a new fuel line my old one was getting realy soft. cleaned out my fuel filters and tested it out ran great on the lake took it to the river no problems that day then the next day it started again. when it happens i can hold the throttle open and with in a few minutes it gets better and were off again or if i let it idel to. i drained my tank also added new gas and isoheet. is there any way i have a fuel pump issue or what any ideas would be great

if your engine gets hot it goes into protective mode it reduces rpms so it wont ruin engine .....it makes it slow and stutters...good stream at telltale? or do u hear an alarm? just guessing as it happened to my 50hp jetdrive...

its pumping water really good no alarm i feel the water and its warm but not hot untill i shut the engine down and the last bit of water comes out do you no where the sensor is maybe i have a bad one and its telling it that

on the side of the head...yamaha.com has the diagrams of yor engine...does it run good again after a 15 min cooldown?

i keep it running at low ideal for a few minutes but once i just left it wide open and it cleaning up and ran 5 miles back to the launch