I went to the museum but didn't see anything. It was far too crowded. I think that the Egyptians are missing the mark in how they handle tourism. They could easy quadrople the entrance price to Temples and Museums (they were seriously cheap) and limit the number of people. They would make more money and people would have a better experience.
I left the Egyptian Museum after about 45 minutes because you couldn't see much due to the number of folks. I bought a book about the collection in the book store and hung out on the lawn outside looking at that. It was far easier to see and a great deal more informative.
I know you will be fine. I was never harrassed but I always went out with a guard. We did notice that the security for our American tourist group was a greatly more extensive than the Aussies and Europeans who were there. We were the only bus that ended up with a chase car, for example.
The bazaar was great. We had fun wandering but stuck with the group. On our one free day, we decided to join our tour guide who put together a tour of Coptic Cairo instead of going on our own. It was a great experience and we got to see a part of Egypt that not everyone does.
Are you doing the cruise down the Nile? That was wonderful. We stopped at 2-3 temples a day. I was in heaven.
Bring your own tea though, they only served Lipton. (sigh)