The modern warfighter operates in an environment that has dramatically evolved in sophistication and interconnectedness over the past half century. With each passing year, the infusion of ever more complex technologies and integrated systems places increasing burdens on acquisition officers to make decisions regarding potential programs with respect to the joint capability portfolio. Furthermore, significant cost overruns in recent acquisition programs reveal that, despite efforts since 2010 to ensure the affordability of systems, additional work is needed to develop enhanced approaches and methods. This paper discusses research that builds on prior work that explored system design tradespaces for affordability under uncertainty, extending it to the program and portfolio level. Time-varying exogenous factors, such as resource availability, stakeholder needs, or production delays, may influence the potential for value contribution by constituent systems over the lifecycle of a portfolio, and make an initially attractive design less attractive over time. This paper introduces a method to conduct portfolio design for affordability by augmenting Epoch-Era Analysis with aspects of Modern Portfolio Theory. The method is demonstrated through the design of a carrier strike group portfolio involving the integration of multiple legacy systems with the acquisition of new vessels.