If the engine sat with water or old coolant in a cylinder, the bore probably rusted and froze the piston in the cylinder. It doesn't take much rust.
At this point I think you're looking at an engine overhaul with oversized pistons if the block isn't cracked. The heads will also need to be checked for cracks. Also plan to replace the radiator at the same time. Clogged radiators are a big reason engines run hot, which is how this started.
You might be better off with another engine, but still replace the radiator.
Try to back-flush the heater core while the work is going on. It could be clogged too.
Did you have a radiator or heater-core leak and ever use a stop-leak product? Rust or stop-leak junk can clog radiator tubes.