There's a function on the wiki that returns the hour of the day. Although you might be better off with the current game time as a floating point days-since-game-start value and doing the math yourself.
http://www.creationkit.com/Function_for_Time_of_Day
You can use http://www.creationkit.com/RegisterForSingleUpdateGameTime_-_Form to get a wakeup call in however many hours you need.
@Justin: well, if everything is done within the effect, it doesn't matter so much.
Externally ... can you not just cast the actor reference as the MagicEffect script in question and access it that way? Much as you'd do with quests?
I hope so or I'm going to need to re-think some plans of mine
