1999 25hp 4 stroke Yamaha... Any ideas??

Does anyone have any ideas.... have twin 25 4 strokes and one engine is cutting out after about 25 minutes of running.... It is not over heating. It cut out the other day so cleaned the carb and still would not go. Put on a spare carb and started fine again... But then cut out again 15 - 20 minutes later... Grateful for any ideas....

Are these engines on Separate portable fuel tanks? The vent screw on the tank that feeds the OB that is dieing is fully open and not creating a vaccume in the tank? If on portable tanks have you checked the fuel pick-up line that sits in the bottom of the tank and checked for any filter that could be on the end of the line that is clogging or clogged from gumming/debris in the tank or tried swapping the tanks from one engine to the other. If none of the above works try swapping the coils from engine to engine and see if the problem moves to the other engine. Coils going bad will fail when they get hot under the cowling. Luckily with 2 identical engines, you can swap parts back and forth and see which part moves the problem to the other engine. Find that part and you found the problem.