Wow massive kudos to you for this project ! Regarding all the references I hope you made it into a paper ! It communicates the complex situation very well. - - To simulate different risks of transmission you could add (invisible or marked) zones in the map that elevate risk (mall, sports, or use a noise map since the patients move randomly anyway). Might over-complicate things but since you mention it prominently under limitations.
It really gets frantic in the later stages and shows how hard decisions fall onto the decider.