Approximately two years after promulgation of the Energy Employees Occupational Illness Compensation Program Act, the National Institute for Occupational Safety and Health Office of Compensation and Analysis Support selected a contractor team to perform many aspects of the radiation dose reconstruction process. The project scope and schedule necessitated the development of an organization involving a comparatively large number of health physicists. From the initial stages, there were many technical and managerial challenges that required continuous planning, integration, and conflict resolution. This paper identifies those challenges and describes the resolutions and lessons learned. These insights are hopefully useful to managers of similar scientific projects, especially those requiring significant data, technical methods, and calculations. The most complex challenge has been to complete defensible, individualized dose reconstructions that support timely compensation decisions at an acceptable production level. Adherence to applying claimant-favorable and transparent science consistent with the requirements of the Act has been the key to establishing credibility, which is essential to this large and complex project involving tens of thousands of individual stakeholders. The initial challenges included garnering sufficient and capable scientific staff, developing an effective infrastructure, establishing necessary methods and procedures, and integrating activities to ensure consistent, quality products. The continuing challenges include maintaining the project focus on recommending a compensation determination (rather than generating an accurate dose reconstruction), managing the associated very large data and information management challenges, and ensuring quality control and assurance in the presence of an evolving infrastructure. The lessons learned concern project credibility, claimant favorability, project priorities, quality and consistency, and critical path project activities.