'00 Johnson 50hp Throttling Down

Just recently, when I'm running at full throttle the motor will run fine for about 2-3 minutes and then it will start to throttle down on its own and throttle back up again. It doesn't feel like a "limp mode" feature because it doesn't stay in the throttle down position. See link below for the video, first throttle down is at 20 seconds.

https://youtu.be/L80a7ZWuTqY

Try a cylinder drop test on it when it acts up.

is primer bulb collapsing? also see you have a fuel filter, most also separate water from fuel, once full they pass water on to carb, (ask me how do i know this), remove and empty into glass jar, see what you get

Great suggestions. I like the water diagnosis. Probably it's going to be fuel related. Do you use ethanol? You must know that it's hygroscopic. Since ethanol weighs only 6.5 lb per gallon it will displace its own weight in water and suspend that in your fuel. So a 13 gallon fresh10% ethanol fuel solution, (what you get at the pump for your car), will hold about a gallon of water allowing the motor to burn it. The filter/separator may trap some of that solution......even more critical as the fuel ages. Ethanol then is trapped which would be mixed with the water in your filter. Why should you know about this? It reduces the effective octane level in the fuel that reaches the motor, and that is not what the motor is engineered to burn. Did you know that pure, non-oxy (clear fuel), weighs only 6.1 pounds per gallon? It WILL NOT suspend ANY water. Then your filter/separator will do its job properly. How do I know this? My son is a chemist, specializing in fuels, propellants, and explosives.