I've come to the conclusion that I should take out the present motor piece by piece and see whats wrong with it.... if it can be rebuilt, then re-installing it piece by piece would be possible and I'd never have the expense and concern
That piece-by-piece approach is not gonna work too well. One of the aspects of diesel engines is that they work off of higher pressures than gas, and require close tolerances and specialized tools to achieve them.
I too would be reluctant to cut thru the hull or deck, but some quick research suggests that at least some center cockpit boats are built with a removable the deck. It would not be uncommon to have to disassemble/remove all the boat furniture or steering or something else prior to hauling the engine.
best of luck,