I’ve seen many threads similar, but none exactly the same as my issue. Twin 496 ho’s, 31 sonic new to me this year. Port motor won’t turn over 4400 and stbd. Runs right up to 4800. Poor running motor serial number is OWO16219, 2004, but cool fuel 2. What I have done already:
replaced plugs and wires
replaced spin on fuel filters and mercury inline filters
cleaned screen in boost pumps
replaced both water pumps with Hardin SS
both motors run about same temp, oil pressure, etc...
replaced # 3 coil after having local merc dealer do a cylinder drop test and tell me 3 and 7 cylinders were dead (number 7 plug wire was off)
motors pull exactly the same until about 2500 and then the good motor is 200-300 rpms ahead which I can make up with the throttles up to about 4200.
got a tech mate pro from rinda last week, no codes, when I just run it on the trailer, it shows 100 % power available all of the time on the “good engine”, on the bad engine, it drops to 60 % as soon as I rev to 1400 with no load on it, and then it will bounce back up to 100... every time I bump the throttle further up, it does the same thing? ... not sure where to go next? I don’t want to just start throwing parts at it? Anyone ever seen something like this before ? Ideas? Advice? Thanks..

Also forget already checked fuel pressure key on, engine off and running .

key on, engine off: 40 psi
idle: 38 psi
1400: 38 psi
2000: 36 psi
2400: 38 psi

didnt go any higher on the hose.

Measure the voltage at the TPS with key ON and motor OFF. See if it voltage change is smooth as throttle is opened

Try not to go above 1800 for no more then real short time, the hose cannot supply enough water to protect the impeller

I can't tell you for certain it is your problem, but the crankshaft position sensor can do weird things like you describe without throwing any codes. If it's a 2004 and the crankshaft sensor has not been replaced, I personally would give that a shot knowing that I fixed a similar issue by doing so.

Also, you should have no issue pulling 5100 rpm out of those motors. You may consider a prop change.

Ok, did the TPS check with the following results:

0 %- .55 v
15%- 1.14 v
26%- 1.56 v
43.2%- 2.23 v
65.8 %- 3.09 v
79.1%- 3.61 v
94.4 % -4.2 v (WOT)

Seems like they are linear, unless you think they are low ?

I saw other posts where that was your issue in the past, and both of the original owners told me it ran (i am 3rd owner) 5,000 all day long with these props.. I am assuming once the 2nd engine is running correctly, it should have no problem pulling those kind of rpm's, i think it is just lagging from the one struggling motor right now.. I am going to try to get ahold of crankshaft position sensor and see if that works. Even thought about switching ecm to good motor and see if the issue follows..? I know not to put good ecm on questionable motor.

Popping in a new Crank Sensor is not going to hurt you. I had my pair of 496HOs for 13 years, and never had a need to swap computers for troubleshooting.

It looks ok, but my comment came from your statement
So was wondering if it did any bouncing when throttling then go back down

Doing all on a hose is not providing real world numbers because of no load

In my prev life as an auto mech, we would use an oscilloscope to check the signal wire on various sensors like MAP's and TPS's. For a TPS, we would monitor scope as the throttle was moved very very slowly and look for noise due to a bad spot on the TPS internal rheostat. Computers hate noise and can cause them to do weird things. Hand-held volt meters won't show noise like a scope will.

I've never worked on a 496 or any fuel injected boat eng for that matter, just throwing it out there since the sensors are very similar to the ones used for automotive.

You need to check pressure under load- driving it. Revving in neutral doesn't require that much fuel and might not show an issue.