I'd want a look at the impeller in case it's on it's way out. In my experience - salt residue is quite difficult to clear, even running Salt Away or white vinegar solution. Could be there's sacrificial anodes on this engine that just haven't been changed or they've simply disintegrated. What about the state of the thermostat too?
If you go down the removing exhaust water jacket and cylinder head route - then have the gaskets available and go easy on the head bolts. If you have access to a heat induction bolt tool, even better, as bolts are notorious for breaking, plus copious amounts of penetrating release.
There's a torque level for tightening and a sequence from the middle of the head out. Don't use power tools or you're on a road to misery.
Davie on here knows Yamaha engines inside out so can advise, especially regards Enduro models. You'll need the model number for correct identification and sourcing parts.
Some interesting videos on Dangar Marine's site on cleaning water passages and changing cylinder head gasket, etc.
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