No matter which way you look at it, trouble ahead
As I warned on Twitter, there should be caution about rushing to think Mohammed Morsi is Egypt's next president. From my understanding from this morning's figures, the difference between he and Shafiq is about 900,000 votes with over 3,000,000 votes uncounted. The Presidential Election Commission says it will not give the final results until Wednesday or Thursday and there is likely to be some contestation by both sides, and perhaps even partial recounts. Ultimately what the PEC says will hold, since you cannot appeal their decision.
So one real possibility is that Shafiq will be declared president and the MB, having already announced its victory, will go ballistic. Or that Shafiq will lose and his supporters will go ballistic.
And then there's the question of parliament. It's still expected that tomorrow MPs (at least Islamist ones) will march to parliament to hold a session on which they will decide parliament's response to the court verdict. Except that parliament is surrounded by army troops who have orders not to let anyone in.
Likewise there is confusion about the state of the constituent assembly — notably whether the one appointed by parliament last week (which has already had walkouts by secular members because of a dispute on its composition) is still valid. When the Supreme Constitutional Court dissolved parliament, it specified that its actions were still valid. There was a law on the formation of the constituent assembly passed last week, but SCAF did not sign it. So it's probably not valid. And SCAF clearly seems to intend to form its own constituent assembly with its own rules, different than those agreed upon in the negotiations of the past two weeks (one sign if the requirement of an 80% approval of the draft text, as opposed to 67%).
Finally last night the Muslim Brotherhood (to its credit) said it does not recognize the new constitutional declaration issued by SCAF as legal or valid. So that's another fight.
So to recap, you have a possible fight on the result of the presidential election, an almost certain fight on the fate of parliament and the constitutional declaration, and a longer-term fight on the drafting of the future constitution. If you're not worried already, start worrying now.
Update: Another way to look at this is that the MB is being forced to pick its fights. It can't challenge on all front, so what will it choose to focus on, the presidency, the parliament, or the constitution? Especially as it has no major allies and very few political actors, including the MB, has a history of acting on principle.
Update 2: I am reminded by Ed Webb that there is case to dissolve the Muslim Brotherhood that will begin tomorrow, adding another threat to the Brothers should they contest the above.