I have a 2003 496 mag ho that runs fine until it reaches 4500 rpm's. It sounds like it is running on 6 cylinders and sometimes it will pop back through the spark arrestor. Starts up and will idle fine. Runs great up to 4500 rpm's, then its like you flip a switch.

update,,, I removed the boost pump, screen was clean, removed the water separator filter and dumped it into a clean container, no water. Removed the spark plugs, they all looked fine, cleaned the spark arrestor. All of the plug wires look good.
Took the boat out again, it would randomly miss at all rpm ranges and clear up around 2500 to 3000 rpm's and at 4500 it would have a dead miss like it was stumbling.

I would check fuel pressure while at speed and pull the plugs to make sure it isn't going lean.
Don't want to burn a piston.
Then move on to other things.

Problem solved. I decided to install new plugs. As I removed the plugs in each cylinder, #6 and #8 were a little different in color compared to the other 6. Installed new plugs and now the boat runs great.

Now you need to find out what caused that issue because it will return. Had that on my starboard engine and it cleared up when I adjusted the timing.

All pcm and ecm 555 timing is non adjustable. One can not adjust timing. The 496 is distributorless.

You might want to plug it up to the computer and find out what's going on. I rebuilt the 427 in my '08 Z06 and had to adjust the timing that way since I put in a heftier camshaft.

Only a couple of places can adjust the tune in a pcm555. I believe it is only 2-3.

Anybody reduce the .060" stock gap to get longer life out of these plugs,coil and wires ?

Just asking.

I found the only plugs to run good in my 496's was the AC Delco OE plug. NGK's would give me a miss at higher throttle. Went back to the AC plug and never had an issue again.

Yep, stock AC Delcos at .060" is the recipe for success on a stock 496. Replaced mine in 2014 when I bought the boat. Whipple tune since 2015. Plan to pull and check/replace plugs this winter.