Having put a new engine into Boracay I can only endorse what others have said, particularly with regard to the exhaust and waterlift
muffler. It's only
money and time.
You may also have to put in new engine mounts and
raw water strainer. This would be a good time to do any necessary upgrading of the
fuel system/tanks.
There are so many reports of
gearbox problems that I'd suggest going with the largest practicable
gearbox. I went with the ZF63 for only a few hundred dollars more. Massive overkill but hopefully it will never break.
I went with the Deere 4045 (Good local support) as Yanmar wanted their own people to do the
installation. It's bigger and heavier but the extra
power is nice.
All other things being equal I'd suggest going with the engine with the largest cubic capacity.