Although domain-specialized FPGAs can offer significant area, speed and power improvements over conventional reconfigurable devices, there are several unique and unexplored design problems that complicate their development. One source of these problems is that designers often opt to replace more universal, fine-grain logic elements with a specialized set of coarse-grain functional units to improve computation speed and reduce routing complexity. One issue this introduces is that it is not obvious how to simultaneously consider all applications in a domain and determine the most appropriate overall number and ratio of the different functional units. In this paper, we illustrate how this problem manifests itself during the development of an encryption-specialized FPGA architecture. We present three algorithms that solve this problem by balancing the hardware needs of the domain while considering performance and area requirements. We believe these concerns need to be addressed by future CAD tools in order to develop more sophisticated application-specialized reconfigurable devices.