This past summer when I was in Egypt with Morocco's tour group, she used Treasure Egypt to handle the tour agency things, and they did a great job. I've also had a positive experience with Lady Egypt.
I have worked with Leyla Lanty's friend Ahmed on several of my trips, and he's great. I had him take me to Kerdassa this past summer to shop for gallabiyas. In the past, he has taken me to Mohammed Ali Street for drum shopping, and Khan al Khalili for gold shopping. When you tell him what you want, he helps you pick a good quality item, and then he negotiates the price for you. At the end, he quotes a fee to you that includes the price he wangled out of the merchant plus a commission for himself, and it's still a lower price than what most of us would be capable of achieving on our own.
You can buy your visa to enter Egypt at the airport when you arrive. No need to get it in advance in the U.S. The first time I went to Egypt, I went to the Egyptian consulate in San Francisco to get my visa, and it was a hassle because I had to leave my passport with them, then return a couple of weeks later to pick it up. Getting the visa at the airport was much simpler. If I recall correctly, it costs about $15.
A big mistake a lot of novice travelers make is packing too much stuff. For a 2-week trip, I take only 3 different outfits, and just keep rotating between them, rinsing stuff out in the sink. This leaves more room in the luggage for purchases!
For ideas on how to stay healthy while there, see the multi-part series on my web site at
www.shira.net/advice.htm . I tackle all the fun subjects - jet lag, diarrhea, catching colds, etc., discussing how to avoid the problems, and what to do if you get them anyway.