Stock 496 HO on a 2005 Baja 275. At idle, the engine runs smooth. Under acceleration it begins to cut out and miss so bad that I can barely get on plane. I've ruled out bad gas as a buddy filled up at the same time as me and he has no problem. I have replaced the fuel filter as well as the cool fuel module housing cap and seals adjacent to the filter cap due to the bulletin from Mercruiser. Took it out today and still has the same problem so I'm wondering if paint chips have make it to my fuel rail and/or injectors. Is there a good tutorial out there that guides a person on the mission of checking the rails and injectors out? Is there anywhere else I should be looking? I figured I'm just days away from call the mechanic and dropping it off.

Just get it scanned.... its easier.

Longshot but - If your battery is old and still has enough power to start the boat it might not have enough AMPs even with the alternator to run. My boat did it 2 years ago and swapped batteries and it fixed it.

Check your grounds.

Maybe Throttle Position sensor or the dreaded crank sensor?

Check fuel pressure.

post the service bulletin

Totally agree with that and run the boat / engine on a remote gas tank with brand new fuel and fuel line with primer bulb hooked to the incoming fuel barb on the engine side