'95 odd starting issue

I have searched the forums looking for similar problems, but decided to throw this out there to see any ideas.

I have a 95 SN, 351 PCM EFI. It starts up fine 99% of the time, but twice now I have almost been stranded far upriver from the trailer. Both times was after running the boat for more than an hour, start and stop, on and off the whole time. Parked it for 3-4 hours and then when trying to start to go home, it would crank but never start. The first time it happened it would actually pop in the manifolds (getting fuel, right?), this last time it wouldn't pop or start for even a second. Here is the odd part: both times it finally started (after 15 mins of cranking on and off, waiting in between to cool off, the battery cables were getting hot) after I removed the plastic cover on top of the engine. It's the plastic cover that says PCM, etc. that I think is only there for looks. As soon as I took it off, the boat fired instantly.

Any ideas what's going on? The first time it happened I thought maybe it was still partially in gear, trying to start under load and I was sitting in weeds. Next time I made sure it was in neutral, in clean water. Possibly a pinched wire under the cover? Bad fuel? Another note: I had been using 10% ethanol (didn't know it was bad until researching on here). I need to get a bottle of ethanol treatment and start using straight unleaded.

Sorry if my ideas are completely off, I'm not a mechanic by any means, but very handy and willing to learn more. I'm looking for any advice.

I was under the false assumption vapor lock didn't happen to EFI. I'll head down that path.

For what's left in my fuel tank, pour in some treatment for the ethanol? What's a good brand that I can find locally?

Oh another issue I had once was my coil was over heating and causing me to not have proper spark. If I let it cool off would start and run ok for a while. Just another possibility

If you have the protec ignition, that would be the 1st thing to suspect.