Could be a few things. Start with the easy stuff.
Look up inside the pump and see how badly the impeller is chipped/worn. Check the clearance between the impeller and then housing, it should be 1/16" or thereabouts. If it's really loose, you may have to re-shim. If shimming is not possible or the impeller is trashed, it puts less load on the engine, allows the engine to run over speed and then the ignition cut limiter turns off the spark momentarily--which could be what you're experiencing. Pretty common on jet drives. If it's really worn you may have to replace the impeller and the sleeve. Welcome to jet drives. The day the motor is bought new is the day it performs the best, from there on out, performance goes downhill until the pump is rebuilt and/or the engine is rebuilt. Jets put a different load on the engine; which is exactly why Yamaha uses a different ECU for the EFI jet 4 strokes than the prop EFI 4 strokes. Others may use similar tactics, I just don't know about them.
Another possibility is a fuel starvation issue. Does the primer bulb suck down flat when at full throttle/full load? If it does, the pickup, line, or bulb could have a restriction (kink?) OR the vent on the tank isn't venting properly. If not, could be restriction between the bulb and carburetor, or at the carburetors themselves.
Could also be ignition related. Sometimes guys will remove/clean carbs and upon reinstalling them, don't bother to check carb sync and ignition timing linkages--both can cause issues, with sync issue causing a rougher idle (most apparent with a prop drive in neutral). Might not notice it much on a jet because it's constantly under a load.
Could also be an issue with the oil tank float, OR overheat warning. I believe both are tied to the CDI to cut ignition if the tank is "low" or the engine's running hotter than the CDI thinks it should be.