Since you are starting off with 2 degrees of downthrust you probably will end up with something between 0 and 1 degrees of downthrust. The thrust line is just a line drawn through the motor crankshaft so moving it 1/2 inch lower will change the thrust line a little but not all that much. There is a horizontal balance and a vertical balance of forces and moments that allow the airplane to fly in a straight line. The thrust angles and incidence angles are an attempt to balance these things. However the balance is usually good for only one speed, usually wide open as that is where most of us fly.

The reason you don't get many answers for this kind of question is that the numbers needed in the equations for the motor is a wild guess, they vary with motor, prop, fuel, etc. It is easy to deal with at the full scale airplane sizes as the motor characteristics are well tested and known.

The changes you are making are pretty small actually. I don't know if I would go to the trouble of calculating angles for the motor. It could be left the same as the original design and adjustments made after the first several flights if necessary. It is what most model designers do based on experience, not on any massive amounts of calculations.