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In this paper we present the first ever systematic design space exploration of microcoded software fault tolerant ion-trap quantum computers. This exploration reveals the critical importance of a well-tuned microcode for providing high performance and ensuring system reliability. In addition, we find that, despite recent advances in the reliability of quantum memory, the impact of errors due to stored quantum data is now, and will continue to be, a major source of systemic error. Finally, our exploration reveals a single design which out performs all others we considered in run time, fidelity and area. For completeness our design space exploration includes designs from prior work  and we find a novel design that is 1/2 the size, 3 times as fast, and an order of magnitude more reliable.