The effect of long-wavelength sinusoidal surface waviness on the development of Tollmien-Schlichting (TS) wave instabilities is investigated. The analysis is based on the compressible flow that forms over an unswept infinite wavy wing with surface variations of variable amplitude, wavelength, and phase. Boundary layer profiles are extracted directly from solutions of a Navier-Stokes solver, which allows a thorough parametric analysis to be undertaken. Many wavy surface configurations are examined that can be sufficient to establish localized pockets of separated flow. Linear stability analysis is undertaken using parabolized stability equations (PSE) and linearized Navier-Stokes (LNS) methods, and surface waviness is generally found to enhance unstable behavior. Results of the two schemes are compared and criteria for PSE to establish accurate solutions in separated flows are determined, which are based on the number of TS waves per wavelength of the surface deformation. Relationships are formulated, relating the instability variations to the surface parameters, which are consistent with previous observations regarding the growth of TS waves on a flat plate. Additionally, some long-wavelength surface deformations are found to stabilize TS disturbances.