Same same with my EFI 200.
New plugs fixed it .
Went through plugs every month

water getting in the fuel

This makes sense.

The boat runs great after launch.....continues to run well for a while, then doesn't (after turning off the big motor and trolling around or a while)

I'd recommend the following experiment:

Water hose to muffs on the outboard, turn on the water. Start and run the boat for your typical amount of time as you would on the lake (I will guess this is 5-10 minutes to your usual first fishing location)
Then turn off the motor for thirty minutes to simulate 30 minutes of trolling motor time looking for fish.....you could turn the water off at this time also.
Then, turn the water back on, and see if the engine starts and runs.
If it does; try the experiment again, this time with an hour of simulated trolling motor time.

The above experiment should provide you with the data you need as there are multiple rabbit holes to explore.......but it sounds like a fuel to motor issue to me if it always starts and runs fine after launch......then fails later.

With that said, if the spark plugs haven't been changed for new ones in over two years, might as well change the spark plugs.

Fresh gas and a portable tank ought to eliminate old fuel, water in fuel, blocked fuel line, and vapor locking fuel system.

I like your thinking on this.

You stated you replaced the "fuel tank fitting" so I assume that included the anti-siphon valve? If not, check that. Next step would be to run it on a portable tank to see if that cures the problem.

I know someone who recently was having these same issues with the motor.

Chased a fuel problem all over the boat.

Ended up with spark plug issue.

Friend has the same problem went to Cypress fished under bridge his boat wouldn’t run the shop said it was carburetor had them rebuilt him and dad went Cofey creak today fished a couple hrs and decided to move motor wouldn’t run. Boat is back at the shop for another thousand…

This ^^^^^^^^^^ I think we know the someone's.

How old is the fuel line?
Ethanol shreds them after about ten years and the plastic plugs things up.

I have new plugs for it. Plan is to install them in the morning and try it again tomorrow afternoon.

I’m going to go with electrical issue. As motor warms and runs a while wire heats up, expands , causes gaps and causes funky issues.

List it in the boats and motors , could not hurt

Dream on....a thousand wont get you [censored] anymore.