A 4.4ltr Isuzu diesel would surely have cylinder liners but you do not mention them.
Usually rebuilding a diesel, the first step is to acquire a full rebuild kit which include the pistons, liners and rings as a matched set.
As for the mechanical rotary injection pump, it will definitely need rebuilding as you state it went into seawater. Mechanical pumps have fine tuning rods, shafts and governors requiring metering, the slightest sign of water ingress can cause all sorts of tuning problems including a runaway situation.
A great resource for diesel engine building is
4btswaps.com look through the Isuzu threads.
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