Onan runs but eventually trips fault breaker

My MDKAL Onan/Kubota genset will run and produce good power for a while, but intermittently shuts off and trips the check engine fault breaker (not the genset fault - that's a different switch).

When I reset the fault breaker, it starts and runs again.

More details/troubleshooting steps:

Last weekend I went fishing for ~6 hours. About 2 hours into the trip I noticed the genset had shut off. I went down in the engine room, didn't see anything obvious wrong, and started it back up. It ran the rest of the trip.

When I got back to the dock, I checked the impeller which looked fine and the sea strainer filter basket which was also fine. I also just had a bottom cleaning so the intake should be clear on the bottom side.

Yesterday, we ran 3 hours from Indian Harbour Beach to Stuart and the genset ran fine.

This morning, we crossed to West End. The Genset cut out after about an hour. At the time, we were beating into tightly spaced 3'+ confused seas. I remember we were also in choppy seas bouncing around when it quit the time fishing.

Once again, I reset the fault breaker and it started right back up. However, this time it only ran for about 20 minutes and died again.

Recently, I had one of my engine exhaust elbows break and fill the engine room with soot. The engine room also got very hot - hot enough to melt the plastic wire chases that all of the wiring runs through but not hot enough to set off the fireboy.

I changed out the main engine air filters, which were totally clogged with soot, but I didn't see an air filter on the genset to change. There's just a black plastic box the parts manual calls a "resonator." It doesn't appear there is any way to take it apart, and its unclear if there is a filter inside. It looks like some people have tried to take it apart and clean it and its just an empty box.

Because this problem started the first trip after the exhaust problem I suspect they are related but its hard to say for sure. It seems like if one of the sensors wired to the fault breaker were bad, the genset wouldn't start at all. And the fact that its happened 3 times now rules out just having sucked up a plastic bag or sea grass or something temporarily clogging the intake

Any suggestions for further troubleshooting?

Copy all re: sensors and thanks for the diagram Capt Ralph. Also good question from Capt J on the heat exchanger. I've had the boat for a little less than a year and haven't serviced the heat exchanger while I've had it. So I should probably pull it off and service it regardless. Anyone know what engine temp would trip the breaker? Next time it shuts off, I can shoot the block at the sensor with a temp gun and make sure its not getting too spicy down there. I'm leaning against that though because the first time it started right back up and ran for 3+ more hours.

Interesting that these sensors can fail gradually I wouldn't have expected that.

Appreciate the tips this should give me enough troubleshooting steps to isolate the problem, and also gives my confidence I'm fine to run it while I'm trying to figure it out.

Ran it this morning for about 90 minutes under load. Couldn't get a temp reading at the engine temp sensor location but here are a few temps (all degrees F):

Oil Pan: 185
Exhaust elbow, hose, muffler: 100-105
Heat Exchanger: 145

All of these seem to be reasonable

Yes when I changed the zinc it broke off in the heat exchanger and I had to remove the end cap to get it out. I don't remember it looking particularly bad at the time. That was about 6 months ago