I haven't done it since 2005, so I can't really comment on the current state of the tracks, but other recent posts indicate that new road construction is progressing very quickly.
I did however ride the Nile route in mid July, and it was extremely hot, definately into the late 40s during the middle of the day. Given you a riding two up, it might be difficult to carry enough water for both of you on the railway track route - at least going via the Nile, there are plenty of small villages where you can stop and get water.
Nile route is also extremely beautiful, and one of the highlights of a trans Africa crossing.
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