I get that some basics are messing with your troublshooting and should be corrected but I'm not sure that these are as intermittent as your symptom. If your fuel pressure is close to regulated pressure, all this other aside, when the surging starts then you are likely feeling the effects of Injector drop out. The intermittence is what takes me there. The heat soak, run time and a myriad of parameters that are involved with injector operation are all happening and the timing of the drop out can almost never be duplicated at will. I have run poker runs where my injectors never drop out and then just playing around on the lake and they drop out. I have also had drop out, sticking and hot soak to the point the boat will not start and all this is injector issues. These injectors are known for these issues and you can pull your hair out trying to pin it down. Checking ohm values when they are hot is one way to see the electronic side. If they are out of the spec range then there is no doubt the injector is bad. With heating and cooling though, it is easier said than done. Also, if there are no-start issues when hot these injectors going bad will absolutely shut the ecm down.

Don't go and try to spot fix the injectors like equipment or automotive repair procedures. Replace them all or one little issue brings the same symptom right back from any remaining "thought to be good" injectors.

Any update from OP on this? Seems at least coincidental that boat ran fine with tank being able to 'vent' via leaking seal...

Bump well what did you figure out on your boat

I'd be very interested in hearing the solution to this as well, I just experienced this same issue with my 502, cool fuel. Same exact scenario, ran fine for the first hour, stopped for about 5 min to unload a friend at the dock, tried to take off and 3500 rpms, no go.
I'm leaning towards aquaforce's suggestion, injectors.
Who's a good source to purchase injectors from on here?

Articfriends 9892137434, he sells new oem and high quality aftermarket

FYI update on solution

A cylinder wasn’t firing. Had to redo the top end.