Howdy Buffo420, I leave my pumps running until the root ball 'chokes' them off, then I un plug them. It may not be necessary to let them run after the roots reach to water level in the reservoir, but I feel that it helps to keep the roots moist and it does tend to promote new root growth. Kind of a "six of one, a half a dozen of the other" situation.
I, personally, do not like to disturb (or damage) the root ball, by trying to remove the pump and lines from the reservoir.