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This is the 2nd of two reports that were created for research on this topic funded through SERC. SERC-TR-2013-032-2 (current report), included the "Software Cost Estimation Metrics Manual." This constitutes the 2012-2013 Final Technical Report of the SERC Research Task Order 0024, RT-6: Software Intensive Systems Cost and Schedule Estimation. Estimating the cost to develop a software application is different from almost any other manufacturing process. In other manufacturing disciplines, the product is developed once and replicated many times using physical processes. Replication improves physical process productivity (duplicate machines produce more items faster), reduces learning curve effects on people and spreads unit cost over many items. Whereas a software application is a single production item, i.e. every application is unique. The only physical processes are the documentation of ideas, their translation into computer instructions and their validation and verification. Production productivity reduces, not increases, when more people are employed to develop the software application. Savings through replication are only realized in the development processes and on the learning curve effects on the management and technical staff. Unit cost is not reduced by creating the software application over and over again. H98230-08-D-0171