RE: Pusher Prop Thrust Line Offset from Datum Line
With your original diagram you'd want the thrust line to be angled somewhat down towards the nose. Likely something like 3 to 4 degrees.
Before you actually take on this rather massive sounding project I'd suggest a series of half size models powered by smaller glow or electric engines/motors to test each aspect. With a quickly built model you could fine tune the amount of "downthrust" angle to achieve reasonably neutrally trimmed throttle changes.