You gave me a link to your code. Do you have a demo so I can see it in action? That will give me a better idea of what improvements to suggest. I am a big believer in keeping things simple. For example:
You have already included gravity, which is a fixed vector, and parasitic drag, which is a function of speed.
Thrust does not have to be complicated. Simply find a maximum thrust that gives you a reasonable top speed after taking drag into account. You have probably already done this.
Lift is a little more challenging because, in an aircraft, pulling back on the stick causes the aircraft to rotate up, which causes lift to increase (as a result of increasing the angle of attack) and which causes an upward deflection in the flight path. But I think you could implement a “spaceship” approach in which pulling back on the stick activates a downward “thruster”. This would cause an upward deflection of the flight path. You would rotate the aircraft up so that the aircraft points in the new direction of flight. So you are reversing the order in which things happen.
These things should give you a fairly simple flight model (perhaps 75% complete?).
You can later make things more realistic by adding induced drag (which is a function of lift), implementing angle of attack and computing the effects of changing air density.