Fergal20, i think you have'n the good point of view in the problem. to make a flight model, you do not have to find out Angle of attack.
AoA is just angle resulting of composition beetween Vxy (Vairtotal projected on {XY} plane), and Vz (still in the airplane coordinates). More exaclty it is : arctan(Vz/Vtotal).
To make your plane flying, You just have to compute forces : P, aerodynamics, inertial applied on your planes, => accelerations => speeds in planes coordinates and if you want to, then you can compute AoA and SideSlip angle ( wich is in arcTan(Vy/Vx) ).
Hope this help
