I have a 2007 Baja 26 Outlaw SST with the 496HO. been dealing with running issues for a bit, Found a couple melted plug wires, replaced them and the spark plugs, new fuel pumps and filter. New alternator,( I know how important voltage is for this engine ) . So proper voltage, No misfires. perfect fuel pressure etc. First couple runs were good. Next trip @ 3000-3500 it bogged down. Backed off throttle and pinned it again and , although very slowly it got on plane and seemed to run fine. Later in the day, boat planes fine, accelerates fine, then when I drop to 3000rpm the guardian alarm goes off again, and I can feel a power loss. when putting it on the trailer at the end of the day it was spitting and sputtering as well. Did the Misfire test at the launch on the trailer, killed every cylinder and felt the dip in the engine with each cylinder shut off. New Manifolds and risers. At my wits end. Any Ideas would be appreciated

Have you ever replaced the crank and cam sensor? The crank sensor can and does go bad without throwing codes.
Do you have any codes?
How did you do the misfire test? With a scanner? Or by pulling each plug wire?
When was the last time you had your fuel injectors pulled and cleaned?
Did you by chance run the tank really dry, and any crud in the tank got sucked up into your new fuel filter or pumps?

Used the Rinda scanner @ 1500 rpm and 3500 rpm. No codes. But its intermittent. Sometimes it runs like a scalded dog, and sometimes it moves like a wounded duck. wouldn't those sensors be constant though? failed sensors usually are failed all the time, not intermittent

Also fuel is clean from what I can tell. Filter always looks good. Kind of the same with the injectors. Not likely to work / then not work and work again. IDFK

I went around and around and around with my pair of 2003 496HOs, with one that wouldn't keep up with the other. No codes.
Replacing the crankshaft sensor fixed the issue, as they can go bad without showing codes. It's electrical, intermittent is it's middle name. It's a magneto picking up a timing wheel; not like a pressure sensor or whatever. Also, the crankshaft sensor is a long plastic "shank". They do get, hot, old, and brittle accordingly.

And IF you choose to replace the camshaft sensor, be aware there are 3 DIFFERENT versions for 496s, and they are NOT compatible. Mismatch can/will even be an interference fit. Do definitely double verify S/Ns before ordering, AND compare, shape, depth and color of the new part when you go to swap.

Neither are tremendously expensive, and at the very least, replacing the crankshaft sensor makes for good preventative maintenance in my experience and opinion.
I have a lot of old posts on here about 496s and this issue I could not pinpoint. "BUP" aka John Mosetti is a wealth of knowledge, but he's not on this forum anymore due to management politics. But he is on Facedork, and here: https://www.boatunlimited.com/
He has forgotten more about the 496HO than anyone will ever learn, IMHO.

Crank sensor:

vortec8100-camshaft-position-sensor-camshaft-gears.html

Will the camshaft or crankshaft position sensors have to be programmed or re-learned? I just mentioned to a buddy who has been helping me with the boat about me replacing both Parts this weekend and he mentioned that there may be a re-learn that needs to be done. Also, I bought the Rhinda scanner. Im diving deep to get this pain in the ass fixed!

Crank position sensor needs a re-learn procedure. I don't think the cam position sensor requires that.

Any ideas on the procedure? Like previously stated I have the Rhinda scanner. I asked the guys at Rhinda about the relearn and the didn’t know or know if the procedure was possible with the scanner. Lots of help