As it looks now, Ayman Nor will be able to run. Not that it makes much difference because they still have the forgery charges hanging over his head. Ayman's trial is due to start on 27 June. There will likely be a break in the middle of the trial and a resumption in September (the presumed month of the presidential election).
But what if the government leaves him be, drops the charges, and lets him run (while carrying on with disruptive behavior until the election and then rigging the results). If Nor got an absurdly low amount of votes (such as 8% of the vote), this could be advertised as strengthening Mubarak's hand. This would galvanize the opposition but I am not sure that would matter.
Well now the amendment of article 76 of the constitution has been institutionally handled, it will be put to a popular referendum (yes/no) vote in two weeks. I am guessing we see more low-90s results.