In this study, a comprehensive methodological platform for deterministic forecasting and uncertainty analysis in the process of innovation diffusion, focusing on knowledge-intensive small and medium-sized enterprises, is developed. Based on the synthesis of the evolution of innovation discourse and system-dynamic modeling, formalized approaches to optimizing fiscal and financial support instruments are proposed, taking into account the stages of the innovation cycle and the impact of sanctions pressure. Hypotheses on the determinants of the effectiveness of tax incentives, insurance premiums and development institutions are verified. A mathematical apparatus is developed based on two-way computational schemes for assessing the demand for the results of interdisciplinary scientific and technical programs.