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Meaningful collaboration among educational stakeholders is crucial in carrying out large-scale, impactful research in K-12 school settings. This process includes developing the knowledge and skills that foster open and informed communication among team members, while also adapting to and preparing for unexpected challenges. We detail our experience of conducting a nation-wide computational thinking assessment study, highlighting the invaluable lessons learned from a procedural, ethical, organizational perspective. Sharing such experiences and challenges may help other researchers gain insights and better plan for future large-scale studies in schools.