Looks that I will check MS flight in case of changes, usually they'll give at least 14 day notice if they would cancel. Last time, air Arabia cancelled my flight but I didn't pay attention, causing all kind of trouble. I booked early morning flight from CAI to ASW, it doesn't say it'll stop at LXR. Bad thing is that I'll have 6 hours long layover at ASW airport connecting to ABS, there is no lounge at ASW, so I'll see if I want to take a taxi to see high dam which is close by. if I were you, I would ask Misr to deal MS flight for me, it won't cost more.
For Nile cruise, the price is fluctuating, offered by viator. I'll have an extra night at Aswan, and have option to buy cruise tickets while at Aswan, but I'll still doing research, so many cruise offerings, it can't be sold out.
In general, I prefer Sheraton over Marriott. But since location is a concern, I'd rather take Cairo Marriott since it's not much more expensive and location is much better. 2 nights of mena house could be an overkill, unless you want to spend a whole day there enjoying the view. I heard that Cairo Marriott is quite unique,, probably not a bad idea to try a night.
I'll send email to ask st Regis, will share with you if they reply.
