RE: Engine Upthrust?
In a new design, I always start out with all angles set to zero. (Thrust, incidence, stab, fusedatum). That is close enough for uneventful maiden flights.
Thrustline and wing incidence are inverse interdependant, but for 3D I would indeed at first stay at zero, because the COG is way back, and the plane should behave the same in all flight positions.
Some side thrust is required to counteract torque and the spiral propwash against the fin.