A peek through the stern tube revealed the center of the output coupling, so I'm hoping that alignment is pretty good. Since my stern tube will be permanently fixed in place with the aid of the prop shaft coupled to the engine, alignment shouldn't be too much of an issue.
The only issue that will need correction - at this point, at least - is a tight spot between two cooling hoses and the foundations. The hoses rub the foundations and will quickly chafe through with the engine's vibration, so I'm going to have to grind out a portion of the foundations port and starboard to give the hoses more clearance. I'm not too keen on messing up my fiberglassing job, but I guess there's no other choice.
With regard to building the engine box, I was hoping that the engine would sit far enough aft that I'd be able to slope the front of the engine compartment aft a bit. I'm not sure just how much slope I'll be able to get at this point, but it's not looking like much. Aesthetically and practically, it would be good to have a gentle slope for the ladder to follow and to free up room in the "galley."