Tilt-rotor quadcopters redirect thrust for translation without banking, but complicate modeling, state estimation, and disturbance rejection. This paper presents a simulation-based flight stack for a \SI{2.00}{\kilo\gram} tilt-rotor quadcopter. The system uses a six-degree-of-freedom nonlinear model with first-order motor dynamics and two-axis rotor tilt, parameterized using a 3D CAD model. A cascaded PD controller commands forward and lateral tilt angles. A 14-state EKF fuses sensor data across hover, early-transition, and transition modes using a hysteretic (Schmitt-trigger) classifier to prevent covariance discontinuities. Because the proportional position loop leaves a steady-state offset under constant wind, a small bounded neural residual is added on top of the unmodified PD controller. It is trained by behavioral cloning from a teacher with privileged access to the true wind, while the deployed network never observes wind. In simulation, the EKF achieves a post-settling position root mean square error (RMSE) of \SI{0.226}{\metre} (horizontal) and \SI{0.03}{\metre} (vertical) and an attitude RMSE below \SI{0.8}{\degree}, and it estimates a wind velocity of $(\num{2.0}, \num{-1.2})\,\unit{\metre\per\second}$ to within \SI{0.15}{\metre\per\second} per axis. The residual reduces steady-state station-keeping error under wind by approximately \SI{49}{\percent}, from \SI{0.117}{\metre} to \SI{0.060}{\metre} at \SI{1.5}{\metre\per\second} and from \SI{0.319}{\metre} to \SI{0.162}{\metre} at an out-of-distribution \SI{3.9}{\metre\per\second}. The framework provides a basis for hardware-in-the-loop and flight-test studies.