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Many DoD weapon systems acquisition programs are exceeding their original estimates for total ownership costs. There are probably many contributing factors to this cost growth, but is Systems Engineering (SE) one of them? How can systems engineering processes, methods, and practices be improved to better control total ownership cost growth in DoD acquisition programs? This paper discusses research in developing an understanding of how SE can be optimized for developing high confidence estimates and better control of acquisition program total ownership costs (TOC). Although this research is in the very early stages, we discuss the technical approach to investigating systems engineering methods and practices related to TOC as executed at one of the Navy's major system acquisition commends (Naval Air Systems Command-NAVAIR). We discuss very preliminary findings and set the stage for further research results.