The problem of modelling the self-consistent interaction of an energetic particle ensemble with a wave spectrum specific to magnetically confined plasmas in a torus is discussed. Particle motion in a magnetic field coordinate system, whose surfaces are perturbed by a spectrum of finite amplitude magnetohydrodynamical (MHD) waves, is described using a Hamiltonian formulation. Employing the δƒ method enables the simulation particles to only represent the change in the total particle distribution function and consequently possesses significant computational advantages over standard techniques. Changes to the particle distribution function subsequently affect the wave spectrum through wave-particle interactions. The model is validated using large aspect-ratio asymptotic limits as well as through a comparison with other numerical work. A consideration of the Kinetic Toroidal Alfvén Eigenmode instability driven by fusion born α-particles in a D-T JET plasma illustrates a use of the code and demonstrates nonlinear saturation of the instability, together with the resultant redistribution of particles both in energy and across the plasma cross section.