As for downtime, I always give the players a little down time between missions (usually a week). Of course, it's sometimes shorter (in the case of a string of runs for an overall story arc) and sometimes longer. (if they messed up a run, the next job takes longer to find).
Also, I let my players dictate if and when they take "time off" from running the shadows (to do those surgeries, get at wiz piece of gear, etc)
so far the most they have taken off is 3 months straight. When this happens, I make them pay out their lifestyle costs, then fill them in on the "word on the street" as it happens. (like the war in/around south America, or the rise of tempo, the out break of a underworld turf war, etc)