Dr. Lynda Stuart’s last day at the Fund for Science and Technology was May 8. (File photo courtesy FFST) The first CEO of the Fund for Science and Technology, the $3.1 billion foundation responsible for giving away a large portion of the late Microsoft co-founder Paul Allen’s fortune, has stepped down nine months after its public launch. Dr. Lynda Stuart, a physician-scientist who previously led the Institute for Protein Design at the University…