Hi all, I just got back from living in Egypt for a year. I thought people might find this advice useful. I originally wrote it for people who were headed to Egypt for a week or two. Don't hesitate to let me know if you have any more specific questions!
1. Food poisoning and water: I personally drink tap water but I am in the minority among foreigners living here. I recommend you drink bottled water as it tastes much better and is extrememly cheap- a small bottle is generally 1LE and a large bottle usually 2LE --although restaurants and hotels will naturally charge more. I tend to eat everything I come across, but generally the advice is to stay away from salads and raw vegetables and fruits unless you can peel them. Getting food poisoning is fairly common for those who are sensitive but my experience has been that when I've gotten sick it has passed pretty quickly. Hygeine standards (especially in restaurants) are pretty low here, and the food poisoning seems to come from expensive meals as much as street food. Basically . . . I wish you luck in avoiding it and try to stay away from raw fruits and veggies.
2. Food! I am also a lover of food and in this respect Egypt is slightly disappointing as the best food is always found in people's homes. However, there are a few things you should try. The traditional Egyptian breakfast is Fuul (fava bean stew) and Ta'amiyya (kind of like falafel but made with ground fava beans instead of chickpeas-- I personally think it is better than falafel, but I've never been to the Levant!). There are fuul and ta'amiyya stores all over the place- the fuul will be best as a sandwich but I recommend getting the ta'amiyya plain as they usually serve it with salad that can be sketchy! (you can say "noss ginay ta'amiyya" (50 piasters-- usually 4 or 5 ta'amiyya patties) or "ginay ta'amiyya" (1 LE worth) to get it plain . . . if the guys just looks confused just say "bidoon sandwich" -- not sure if you speak any arabic, though even if you do the Egyptian dialect is rather different that MSA or Levantine Arabic) .
As far as dining, you should to to to Abou Al-Siid. This is in Zamalek by Diwan Bookstore on 26 July Street. I recommend the "Molokhia" with rabbit or the "Fatta" . . . this is the closest you are going to get to the kind of food served in Egyptian homes and the atmosphere is nice. Its popular among upper class Egyptians and ex-pats. You might have to call ahead a day or so to reserve as sometimes they get busy. The phone number is (02) 735 9640.
Most of the other nice places in Cairo tend to be Lebanese or Western (or horrible attempts at Chinese/Korean/Japanese food . . . which obviously won't be of interest as you are coming from the Bay Area!) restaurants. For Lebanese I recommend a restaurant called "Dar Al-Amar (Moon Deck) on the Blue Nile boat in Zamalek (your hotel should be able to direct you there-- a taxi there from anywhere in Zamalek should be 3LE, but they'll probably want 5LE as you are tourists)-- I recommend the hummus and the hot hummus though if you have traveled in the Levant you've probably had better! Another decent Lebanese restaurant is Sabaya (or is it Saraya??) in the Intercontinental Hotel downtown (the big Pink-ish one on the Nile just off of Midan Tahrir) but I recommend sticking mainly to the appetizers as the main courses (especially the meats . . . mine were overcooked and tough) are a little disappointing. I loved the raw lamb with cracked wheat and their apple tabouleh is really good (it is a salad, but since this is a hotel I think (hope) it should be okay!?). Also decent is "Studio Masr" on the Nile City boat (next to the Blue Nile boat in Zamalek). They serve Egyptian food, specializing in meat and I think they do a fair job, but the quality of the food is here is nothing compared to the kinds of things you are used to in the Bay Area!
Also, you have to try Koshary while you are here. A good place for it is Koshary Tahrir which is on Champollion Street about a block away from Midan Tahrir. If you are walking from Midan Tahrir it will be on the right side of the street. A small bowl is 2LE however this might not be great for your wife as Koshary isn't the most sanitary! I think this place is listed in Lonely Planet.
My NUMBER ONE tip for eating well in Egypt is to make friends with Egyptians and eat with them-- at their homes or places they take you. Even if the food turns out not to be so great the experience will be!