We have a new to us boat that was experiencing the classic cool fuel issues of shutting down and not starting. Then 45 minutes later everything is fine for a few minutes, then repeat. I have both engines out for other reasons, and pulled apart the fuel coolers.

I was expecting to see paint flaking all over, but everything inside looks perfect. Not a spec of missing paint on the top section or bottom section. What I did find was corrosion on the water coolant inlets and outlets. I cleaned those the best I could, and tapped one of the coolers for 1/2 pipe thread.

The question is should I try to flush out and then use the used parts? If we were talking even 500 dollars a piece I'd just buy new. However from what I read, mercury never really fixed the problem, just changed to 3/8 threaded fittings for 1200 a pop. So in theory if my 1/2" threads seal, I would have the same thing as new without spending 2400 dollars.

What actually happens when they overheat to stop them from pumping fuel? I'm not sure if the ECU just turns them off, or the pumps vapor lock and keep building heat. In other words, are the pumps likely OK, or shot. Buying new pumps puts be back to just replacing the modules. However, I know both engines ran when I took them out.
What are your thoughts on running the units if I get them all re-assembled?

Doesn't sound to me like a paint in the fuel issue. might be the fuel pump stops running or an electrical issue, but don't see waiting 45 minutes and it starts back up being fuel.

What motor and serial number?
Are there any codes?
When it stops running and turning key OFF and back ON, do you hear the pump run and 2 beeps?
What else takes place when it does not run, voltages, power, other?

These are 496 MPI's, don't have the serial number offhand, but 2007 vintage.

The pumps were for sure over heating, the coolant passages were all but clogged. Shutting down for 45 minutes lets them cool, then they restart just fine.
I did not hear them running when the key was turned and they were "hot". That is why I was curious if the ECU kills power to them, or the pumps just don't work. The question is why wouldn't they spin?
Then, when cold, everything is fine. Most mechanics said it is exactly what they do when they overheat, and I found 100% conclusive evidence that the coolant entry and exit were clogged.. it's the older plastic tapered fitting and oring design.

thats a common issue as well. Been taking place for years especially in high mineral content waters and saltwater. Or even sandy waters.

The cool fuel will shed paint regardless - you just have not dug deep enough - the top section needs to come away and so does the regulator and so does the dampner. Its shedding starts in around a 8 to 12 year mark for an average timeframe. NO way around it. The top section by far is the worst for any of the paint shedding and other crap.

Since there 496's I'll leave the answers to BUP, but still don't see a fuel pump overheating and to stop pumping, then when cooled down all is good again without issues

over heating fuel pumps can be a voltage issue as well. Also a fuel delivery issue causes the same. Fuel itself lubes and cools the fuel pump but needs the volume to do so. Also the boost fuel pump can starve the high pressure fuel pump inwhich causes both to over heat. .

Air in the fuel stream in which causes fuel pump cavitation - that overheats the fuel pumps.

Weak fuel pumps

restricted fuel pumps and or restricted fuel system any of this will over heat fuel pumps

If your boat shuts off that is an easy test to find the issue. Run a fuel pressure testing gauge to monitor psi and the engine shuts down what is the fuel pressure then and or how fast does it bleed down.

Also have a scan tool hooked an monitor voltage thru out and when the engine shuts down what is voltage and YOUR 5 V reference voltage ??????

Your app would not be hard to fix. Possible ground issues can be the main issues here inwhich cause voltage issues and or fuel pressure and or fuel delivery issues.

if the engine shuts down all by itself it will throw fault codes so what code(s) has faulted ???

I couldn't get to much information, we were on a sea trial when this happened. Fuel pressure goes to zero, engine's stop running. We took the cost of two fuel cool modules off the boat, I was just wondering if I had any salvageable parts.
So from what you're saying the paint will flake... better off just going brand new.