Despite unofficial returns showing Morsi ahead by close to a million votes, the Shafiq campaign are reporting their numbers show them ahead, so both sides are currently celebrating. And according to Al-Shorouk, SCAF has just appointed a military man as Chief of Diwan for the President of the Republic, the kind of appointment you might have thought the President himself would get to make.
At this point I think almost anything could happen. [UPDATE: They've also named a new "National Defense Council" with its membership specified (and unlike SCAF, including the President), but with its actual responsibilities, duties and powers unexplained.]
Normally, I don't hold much faith in political scientists who rely on models, but I think Marc Lynch's interpretation of Egyptian politics in terms of Calvin and Hobbes is not only brilliant but possibly the best way to approach developments right now. If you haven't read it, do so. SCAF is clearly playing Calvinball right now.