496HO, runs fine below 4k rpm but starts "missing" above that, almost like a car would if it had a bad plug. Switched out new fuel/water separaters, trying to avoid a new pump but starting to look like i may try that. I put some star-kron in the fuel to see if it was just bad gas. It didnt seem to help. Any suggestions??

Have you checked the plug wires? I had a plug wire pull off part way off of a coil on one of my 496s & it started missing at high rpm.
randy

My Starboard engine was down on power, very noticeable above 3000 rpm. I purchased diagnostic software and with the ignition coil 'misfire' test was able to individually cut-off spark to each cylinder. This identified #8 was not firing at all and #1 was sporadic. I changed both spark plugs and the problem is fixed. I don't run the engines hard and idle a fair amount so most likely plugs got loaded up....a bit surprising to me but this was my issue for what it is worth. The challenge is to troubleshoot these engines without the software. If you have a 'side by side' installation, you certainly don't want to be changing plugs and wires etc, not knowing what cylinder is causing the issue considering how difficult access can be..... hope this helps....

Do you have inline "bullet" fuel filters as well? They are about 5" long, silver; about the diameter of a stick of pepperoni. These need to be changed too.

Untreated ethanol fuel can and will destroy the fuel pumps on 496s. I know this from personal experience.

Plugs and/or wires is where I would go next, but I highly recommend checking it out with the a Rinda scanner or the software. Rinda Technologies Inc. Marine and Industrial Engine Diagnostic Tools
The scanner is money VERY well spent on these modern Mercury motors with Smartcraft. You can go in with a few friends/neighbors to buy one and share.

I do not have the in-line filters, i was surprised at this... Will be changing plugs today or tomorrow and draining water separaters... Going to take the fuel pumps off again and inspect the screens, as last time i had some crud in there.
Thanks for the help!

AJFish...pull your bananna out of the tail pipe...they tend to run better.

I would run all of the gas out of the tank first. My old 496HO would miss, and only at the higher RPMS, if the gas had sat over winter, or once when I'm sure I got crap gas. The next fill up it ran fine.

Jeb you are a homo, lol

Ignition problem needs to be diagnosed...

AJfisher and myself swapped fuel pumps side to side and the problem followed. He also pulled out the bannana. Theory is the ethanol wrecked both pumps over the winter.