Dwayne makes some good points. Another thing to consider is that on average a "rebuilt" engine will probably only have about half the life of new. Also, don't forget that unless you replace the starter, injection pump, fuel pump,alternator, cooling pump, raw water pump, etc, those things will be "old". Did the price comparison you did include replacing all of these with new ones? I don't think you would run into a lot of the possible problems if you stay with the same manufacturer (Yanmar), they should turn the same direction etc., you will have to compare where everything is on the larger engine to see if there will be major problems.
SV Laurie Anne
1988 Brewer 40 Pilothouse