The acid-catalyzed deprotection of glassy polymer resins is an important process in semiconductor lithography. Studies have shown that the reaction kinetics in these materials is controlled by slow diffusion of the acid-anion catalyst, but trends deviate from models of a first-order reaction coupled to a composition-invariant Fickian diffusivity. We present a concerted experimental and computational effort to examine catalyst diffusion in a model resin of poly(4-hydroxystyrene-co-tert-butyl acrylate-co-styrene), or P(HOSt-tBA-St), which is deprotected in the presence of an acid catalyst to poly(4-hydroxystyrene-co-acrylic acid-co-styrene), or P(HOSt-AA-St). We employed an inert catalyst analogue to examine long-time ion dynamics in both terpolymers with atomistic molecular dynamics simulations and compared the calculated Fickian diffusivities with direct measurements of ion diffusion fronts using time-of-flight secondary ion mass spectrometry. Our results demonstrate that ion diffusivities in P(HOSt-tBA-St) and in P(HOSt-AA-St) are similar near and below the glass transition, consistent with a diffusion process that is dominated by interactions with the polar HOSt units. We then compared the bulk reaction kinetics measured by Fourier-transform infrared spectroscopy with reaction kinetics obtained using mesoscopic reaction-diffusion models. We found that initial reaction kinetics is significantly accelerated compared to predictions based on the long-time ion diffusivities of our inert system. This study highlights the potential of atomistic modeling coupled with targeted experiments for interrogating the physical and chemical processes that control pattern formation in next-generation lithographic materials.