I like the idea of using the irrigation timer personally. I have heard that starting and stopping magnetic pumps can be iffy as to if they will come back on (that could be totaly crap I dont know for sure).
I dont know any reason to turn the pumps down when the lights go off. The fish will be fine at night even with high flow. They will probably just find somewhere in the
LR to camp.
Most corals eat at night and I would think flow would be most important at night.