Not sure if it's too late but I used the Lonely Planet Egypt guide and found it indispensable combined with recommendations from wikitravel. If you really want to get in depth (even for reading after the trip as well) then I wholeheartedly recommend getting Caroline Williams' Islamic Monuments in Cairo.
Keep in mind that south of Cairo (especially Luxor) most of the major sites are going to be ancient ones but Aswan has an awesome Fatimid cemetery and the Nubian museum which covers more recent history as well as ancient. West Aswan also has a cool medieval monastery that aside from the guards was completely empty when I visited. If you're planning to visit Alexandria or anywhere else in the Nile Delta let me know and I can recommend stuff there as well!