Training a task-specific small reasoning model is challenging when direct human supervision or high-quality labels are scarce. However, LLMs with reasoning capabilities produce abundant intermediate reasoning traces that can be systematically refined to create effective supervision signals. We propose Reason-Refine-then-Align (R2tA), which turns refined model rationales into supervision for training task-specific reasoning models. Our method generates initial reasoning and responses from an open-source base model on task-specific inputs, then refines these traces, fixing hallucinations and inconsistencies, to form a high-fidelity dataset. We perform a two-stage alignment, supervised fine-tuning (SFT), followed by direct preference optimization (DPO) to calibrate the model's intermediate reasoning with human-validated conceptual preferences and then condition the final output on that aligned reasoning. As a case study, we apply R2tA to evaluate extended entity relationship diagrams (EERDs) in database system design, a structurally complex task where prompt-only methods miss or hallucinate errors. We curated a dataset of 600 EERD variants (train/test split of 450/150, respectively) with induced mistakes spanning 11 categories. Empirical evaluation suggests R2tA provides a practical, cost-effective path to scalable LLM adaptation in data-scarce domains, enabling reproducible AI tools for education and beyond.