i'd stay away from 'remanufactured.' $3000 for a 'remanufacture' with unknown quality, vs. put 2000$ into what ever parts to rebuild what engine you've got. put your boat on the hard for a year, find a trade school near you who teaches diesel mechanics, and front the cost of the parts. unless you freeze-cracked the block, it should not come close to the cost of a whole new engine. ( as to the the tranny gearbox on the rear of the yammer engine , it's hard to imagine what would wreck both the tranny and the engine simultaneously so you'd need a total replacement...)
as to replacing that model engine with some other manufacturer's model: you'll need to make sure the different model works with your existing prop and raw water seacock , and can fit in your existing engine compartment. and you'll likely have to redo your engine bearers. and since you'll be disconnecting the prop shaft , while you're at it replace your Cutless bearing.
