Coastal Marine in Seattle wants over $20K for a complete rebuild, total reman, engine tore down to the last piece, when you get it back it looks like a new engine. I know this because I have talked to them about rebuilding my 41a's. Parts alone is a minimum $5,000. Liner kits are $700 each, the pistons are a better design to reduce smoke, 41a's are known to make smoke when not up to operating temp.
I would love to replace these with a different brand but I'm not having much luck finding choices.
oottomc do you have a reduction gear or an outdrive? When you say "skiff" it makes me think of a small seine skiff.
I have a 36' aluminum bowpicker and one of the likely swaps has been YANMAR .