I will answer my own question since I just was in Aquaba. There are actually at least 2 ports from which you can depart to Egypt from (Sinai Peninsula) – one closer to south beach and one in actual Aquaba. There are slow ferries and fast ferries and from what I could gather the time takes about 45 minutes to 2 hours to cross the Red Sea depending on which speed ferry you choose.
A minimum 1 night stay is required on the Egypt side of the Red Sea. The price is very expensive – somewhere between 90+ Jordanian Dinar for a ONE WAY ticket only. There is usually a morning and an afternoon crossing but schedules may vary depending on the season.
You can find more info here:
http://www.abmaritime.com.jo/main.html
Regards,
Dave