A couple of problems you may run into with using an outboard, even a long-shaft version on an outboard bracket, is that most boats will have a problem with keeping the prop of an outboard, mounted at the stern in the water. You might be better off using an outboard well, a bit further forward. Not only would this prevent having the 100 lbs of outboard hanging off the very stern of the boat, but it would probably allow it to grip the water much more efficiently. A marine surveyor or architect can give you a better idea of how well the boat would work with a stern-mounted outboard. The stern would probably also need some structural reinforcement to handle the weight and power of the outboard.
I would strongly recommend that you go for a four-stroke design, as they are quieter, cleaner, and more fuel-efficient than the two-stroker varieties.
You don't mention the length, displacement or size of the vessel in question, or how large the Yanmar diesel that you are looking to replace was. The horsepower to boat size ratio of diesel engines to gasoline engines isn't quite a linear one, as the diesel engines generally have a lower rpm and higher torque curve than the gasoline engines.
Most outboards have a very limited selection of props they can be used with, and finding one that has the appropriate pitch and power rating for your boat may be an issue.