Simulations of over 10;{3} hydrodynamically coupled solid spheres are performed to investigate collective motion of linear trains and regular square arrays of particles suspended in a fluid bounded by two parallel walls. Our novel accelerated Stokesian-dynamics algorithm relies on simplifications associated with the Hele-Shaw asymptotic far-field form of the flow scattered by the particles. The simulations reveal propagation of particle-displacement waves, deformation, and rearrangements of a particle lattice, propagation of dislocation defects in ordered arrays, and long-lasting coexistence of ordered and disordered regions.