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Issus with 350 mag mpi on a 270 signature 2010

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I explain our problem:
The engine (350 mag mpi 2010 with 460 hours) starts well, runs well before 2000 rpm and seems ok after 3000 rpm. However between 2000-3000 rpm, the engine "coughs" and seems to have misfires only when it is forcing (in neutral everything is ok)
We have carried out the following works / changes:
Changed: the 2 batteries, the 2 fuel filters, the spark plugs and the wires, the distributor cap, the rotor, the iac, 2 sockets and unplugged the wiper which works without stopping otherwise ...
In addition: the fuel is okay (no water), the compression is good on all cylinders, the fuel pump pressure is good and no error code on the computer ...
Nothing works and our mechanic is at the end of his knowledge ...electrical problem?! ???
Thank you if you ever have any ideas that could help us ...
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Bad running at 2000 to 3000 rpms ONLY. When the boat is moving in gear.

Engine checks out O K otherwise.

This condition would typically be a sticking vacuum advance. Sticking centrifugal advance.  But with today's load  of sensors ?  

Have your mechanic CAREFULLY connect a timing light to the engine to see what the timing is doing during the missing in forward. 

The boat MUST BE TIED TO A STRONG PIER !!!!!!!!!  You will hopefully get the condition to occur .   WARNING !!!!!!!!!!!!  STRONG ROPES TO STRONG BOAT CLEATS !!! USE ONLY THE END OF A DOCK !!!!!!!!!!!!!!!!!!!  If the boat breaks loose ?  TURN THE KEY OFF !!!!! fastest way to stop the prop. 

Does the boat have 1  or   2  engines ? If 2 ? You said 2 fuel filters.  Only run the bad engine . Less strain on the cleats. You could rip them out . They are not made for lots of power.

The purpose of this test is to eliminate  a ignition system problem.

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If the test proves the ignition is O K ?   Great Only the fuel system to do.   

I will guess That the computer is CONFUSED at those speeds.  That could be due to the fuel curve in it being changed . Who knows ?  Sensors  ?  Resistor checks of all of them.

Hopefully it is not something like a loose sensor connection that vibrates loose at those rpms.  The removing & testing of each sensor will repair a loose sensor.

If none clears it up ?  I would send the computer out for a check out & reprograming.

1 other thing.  Run the boat in open water FIRST at 2500 rpms for at least 2 minutes. stop the boat quickly. TURN OFF the engine . Check each sparkplug . One at a time . Look for a ODD COLORED one.  Have to go. Doctor. be back.

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Clean your throttle body!  Remove the flame arrestor, open the throttle body and wipe down the inside of it with a rag sprayed with carburetor cleaner.  I threw thousands of dollars of parts at mine with no success until I tried this remedy.  A Florida boat mechanic knew exactly what the problem was when I described similar symptoms.  He was right.

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2 hours ago, Joumax said:

Problem solved !! It was the rotor, it was not in the wright position .....

Glad to hear!  After my issue, I ran the motor for probably 10 hours without another misfire.  Then, after another mechanic did some work on the boat (unrelated to the motor), it developed an entirely different type of misfire.  I took it to a trusted mechanic and he told me he reset the timing and it has been perfect ever since.

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