I have twin 496 hos , port motor exhaust on port side has very little water coming out. Triggering the manifold temp alarm, I have back flushed system even took riser off to inspect and flush? What I'am I missing or has anyone else had this issue?
I replaced both water pumps to the stainless steel Hardin model, but have put a few hours on with no issues before.

Have you cleaned out your Heat Exchanger?

Yes I back flushed it, and replaced the gaskets. I have pulled off each hose to make sure water flow as well.

Not that it should trigger an alarm but the port side usually does run warmer, particularly when running on the hose. Do you have a water pressure gauge?

I have been backing down the ramp and starting it, I do have a water pressure gauge. That motor has been running lower psi so repalced the sensor and same result?

Have you checked your transom assembly hose for blockage or perhaps zerba mussel growth?
Some folks have seen collapse and corrosion in this area that has needed to be replaced/addressed.

Also, do you have a fresh water flush system? Sometimes there are parts in that system (the Tee into the sea water line) that get's gummed up with debris.

Yes I checked that as well, Have anybody ever seen the exhaust drain fitting fail, I see there is a check ball in it??

I have not, but hopefully "BUP" will check in.

Question: How deep are you backing in the ramp when you evaluate? Are you going in just enough to get the pickups wet, or are you backing in deep enough that the water pump is in it's natural position with the SWP at or below the lake level? I'm just wondering if you have a suction/air-leak problem somehow.

yes for the check valve or check ball however one calls them for owners. Easy testing here. take them out of the mix for testing only and use clear hose in place so you can watch for flow volume and air bubbles. one can go thru the cooling system per area with clear hoses to narrow down the problem by using clear hoses - they are used for testing only - as you replace the rubber cooling hoses is sections of the systems.

Back flushing sometimes is NOT the total way to clean out the cooling system. Have you check the oil cooler for restrictions meaning looked in there really well.

Are the end cap gaskets for the heat exchanger NEW ? Brand New ?

Exhaust manifold and rises internally in good shape with no restrictions ??? and all your gaskets and tabulator installed correctly ?

Condition of the cooling hoses - any collapsing or creased ? causing cooling water low volume output and restrictions ?

you can by pass the drive and the transom side for testing - big bucket of water next to the engine - buy an extra long hose to replace the inlet hose from the water impeller housing - stick your new long hose in that bucket of water and run the engine. check to see -- Did the output water flow volume increase ? You can test the water flow volume by collecting it out the exhaust to compare all your test results.

had to add --- do you have a dry engine compartment and bilge when you run the engine and shut it off ???? or do u get water collecting in the there even running the engine on the water hose ???

Watch out for the air actuator system and its drains as they can be a problem child for leaking water and or leaking air into the cooling system.