1995 SS GT-40 Runs like crap when the thermostat o

I have a 95 SS with the GT-40 EFI engine in it. A "friend" took it out with his family. We keep it at his dock. He said he went out to run it, he cranked it up and noticed water slinging around in the front of the engine, he did think anything of it so he ran the bilge pump and went back up to his house and left the boat running.. We later discovered that he left the boat in the water for an extended time. We forgot to put sealant in 4 holes in the back of the boat that bolts held plastic covers over the hooks.

Anywho, he says he's out, the boat is getting poor fuel economy, he says there is more smoke than usual coming out the back. and the boat is loosing power. He almost gets back and the boat shuts off. He is not very good at explaining engine issues or symptoms.

So I got out and check it out. It try to crank it and it sounds like an 80 year old man with pneumonia, its couching and backfiring, wont run.
So I pull the plugs and decide while I had them out to do a compression check
115, 112, 115, 110,80, 120, 115, 110, 95 PSI
So I replace it with new plugs, replaced the fuel filter, it fires right up. Runs just like it always did, until the thermostat opens, then it starts running like complete crap. Its spitting and sputtering, it has a racing idle, and it dies, after it dies, it will crank right back up.

The plugs in the low cylinders looked brand new when I pulled them out, they were just as white as white could be, indicating to me that its possible water is getting in there somehow.

Anywho, just wanted to know what you guys thought, Thanks

Sounds to me like it may have got hot and damaged the head gaskets. I hope that is not the case.

Wow, you get right with it when you have a problem. I did not know aluminum versions of the GT40 heads were available. Glad you got it fixed.
One thing to look for in the old gaskets is any sign of burn through, usually in the narrow area between cylinders..