the move to ban someone from running on the grounds of a period in jail during the Moubarak period would be considered abnormal and a little bit fishy and undemocratic.
This. Very much this.
Try and imagine the uproar in West Germany if the GDR had tried to impose such a rule for the march 90 elections (for parliament, not a Presidency, but still.)
It's really a very telling sign of just how much power the old order (and that means the military, mostly; at least as far as one can tell from the outside) still has despite Mubarak's fall. The democratic revolution is not complete, at least not yet. (And Western governments are evidently quite happy with that.) That doesn't necessarily mean more violence is needed; it may well happen gradually after the election.
I'm hoping for the best for your country's future, Mahmoud.