Okay a little history, Around the 4th of July, bad backfiring and rough running, tuned up, changed all filters and had injectors serviced (the real problem)... boat runs better then ever.

Just after this take the boat out, temp runs up to a little better then 190 degrees after about a 20 minute ride, shut it down, jumped in figuring I caught something in my drive, NOTHING. Continue to destination with no problem, heading back boat runs fine til I come off plane, then it heats up quick sputters and dies, with the guardian thing going nuts. restart and it runs well and cools off.
Since then I have done the following,
Cleaned heat exchanger, with muriatic acid, looks like new inside.
Back flushed, forward and sideways flushed every raw water hose and port.
Changed impeller.
Took out thermostat.
Flushed everything again.
Ran with coolant cap off in hopes air was in the system.

It warms up running, seems to cool off at idle, shoots plenty of water out of exhaust, the water pump on the motor looks fine is not leaking or anything, I am at a loss.

Two questions.....did you take the heat ecxhanger off to clean?

Where is the thermostat on a 496?

Not that these are related to your issue, I am just curious.

HA! Yes took heat exchanger out to clean, Thermostat is under the heat exchanger on the port side.

Impeller housing scorn or grooved? Also water circ pump needs to be changed? Also air entering into the coolant system you can check this with a clear hose in the place of some of other coolant hoses - look for air bubbles.

Also the incoming water connector is plugged / bad / cracked , its the one inside the transom assy inwhich the incoming water supply hose is connected to. Does your boat sit in the water for any lengthly periods? Good luck

Circ pump is what i'm thinking, but is there any way to check it?
Clear hose is a great idea. The engine is putting out more water then I've ever seen it. It only stays in the water a day or so at a time.

water circ pump - rust stains trailing from the bottom weep hole is a good check also weep hole drips water while running motor or drips when after engine is shut down. Hope this helps. got to run.