I'm quite sure you'll be fine with your F650... I've just ridden to N. Ethiopia on a Dakar. If you've got the bucks, it's rewarding to replace the fork springs and rear shock...very rewarding.
Otherwise, I'd e-mail Jim under the Yamaha pages in the HUBB. He's from CT, and failed to get into Egypt. Egypt doesn't take SA carnet I guess. Anyway, contact him for some advice. Otherwise, I guess you could put your bike on a ship in Djibuti (yes you can ride there with no problem from Ethiopia) to get around Egypt.