Thank you for the additional information.
1.) Are you saying one engine does not rev above 4500 and the other revs to 9000? Also, for simplicity, which engine, L or R, revs to 9000?
2.) If this happened after trying to back it off the lift, have you inspected the clam shell that is used for reverse? I am curious if they are both clearing the jet stream when shifted into Forward. It should be very obvious if one is not moving as much as the other. When in Forward, they should completely clear the pump nozzle. For this to be the problem, it would have to block almost half the nozzle. Just pointing out we are not taking a difference of an 1/8", but more like inches.
3.) When you said you checked the intake valves, did you pull the clean out plugs and inspect the pump and impeller or did you go under the boat and check the intake grate?
4.) Another thing to look at is the air filter element for the affected engine. Make sure it is not oil saturated.
5.) If you have not pulled the spark plugs out to inspect them, now is the time to do that. Especially compare the spark plugs from the engine that revs up compared to the ones that didn't. IF possible, if you notice a difference between the two, I would like to see pictures of each.
The cooling system should not cause this, especially if you are not seeing an alarm or warning that it is going into overheat mode. Similarly, the spark plugs are not going to fail because it was revved in reverse. The engines never change direction of rotation for reverse. It uses those clam shells I mentioned previously to redirect the thrust forward, producing reverse, instead of allowing it to have a straight shot out the back. I would not have suspected any sort of weeds or anything in the jet pump either. Anything like that wrapped around a prop shaft would produce high RPM's with no acceleration. Since the problem is one engine failing to rev up, that would not be the case.
There is a very remote possibility that something solid and large got sucked up into the jet pump in between the intake grate veins and bent the prop blades. The probability is incredibly low, but exists. I suggest checking the other things first.