I don't think you are going to find an engine with a lower profile that you could install with available parts. Put a 350 in there. Max HP on that drive is recommended at about 280-300. Alpha Gen II maybe a little more.
A low profile intake and short flame arrester should do ya. Get into the engine compartment and close the lid. Then you can measure how much room you really have under it above the engine. Any more than 1 inch above the flame arrester is a waste, in your case, anyway.
Edit: Unless this boat was built in the late 60's/very early 70's, it is most likely GM powered. 5.0 could be a 302 Ford or a 305 Chevy. You don't say which specifically.