I just pulled the head and found rust in the combustion chamber (opening for injector and the valves) in the cylinder closest to the crank (away from the tranny). Also the water jacket openings in that area are clogged. I'm going to soak everything and hopefully free up the piston and remove the rust on the head. Assuming there is no permanent damage, I need to clean out the water jacket. Does anyone know of a suitable way to do that without removing the engine and boiling it?
Best way to 'de-salt' the engine is to put in RydLyme into the fresh and raw water cooling loops. .... for a flush of the raw water side, just extend the inlet into the same outlet into a bucket and 'recirculate'. - Rydlyme is an inhibited acidic solution that only attacks/dissolves the carbonates and NOT the base metal of the engine.
www.rydlyme.com/ DO NOT use muriatic (hydrochloric) acid as it will also remove engine base metal.
Once you get the head back on then pump in the Rydlyme. Or you can take the head to a 'radiator shop' that does ultrasonic cleaning, clean out the head passages with ultrasonic cleaning, then reassemble and do the whole engine and exhaust manifold with Rydlyme.
Make sure that you can identify if and where the head gasket was leaking .... if you cant, suspect that physical altitude of the eshaust exit to the wet muffler is TOO LOW ... and if so then consider to install a 'dry stack' on the exhaust to prevent 'suck back' from the wet muffler. If/when you find a rusted exhaust valve (or rusted exhaust valve stem) - consider that to be symptomatic of a fairly strong possibility that the engine 'sucked - back' water from the wet muffler. Do you have a siphon break on the water injection loop???? if not consider install one.
A 'dry stack' should elevate the physical 'highest' place in the exhaust system (that portion of the exhaust system that is 'upstream' of the wet muffler.
To get this engine turning .... consider to follow the outline previously posted of using MMO in the cylinders .... so you dont break the piston rings. This 'MMO soak' will work even with the head removed.