maybe one of the builders on forum can tell you better about engine box question, i can say there is fair amount of room in the bilge for a good size diesel such as an older DD, with the newer, smaller, lighter engines such as the Yanmars i can see it could be flush with sole. if you IM me i can send you a name of a reputable surveyor out of Fairhaven, otherwise ask around and/or look for professional accreditation such as SAMS, ABYC designation, there is no license that i know of.