It's a 24 hour airport, so I don't see any difference in your travel being at night.

Your journey should be do able as myself and others described.

Yes, you should be able to check in on line however the website won't issue you an on line boarding pass for the departing Cairo leg, but it will give you a "check in receipt" which you can exchange for a boarding pass at the transfer desk, as described above. Either have this receipt or a paper copy of your onward ticket itinerary printed out (on available on your phone) to ease the transfer, as already described above.

Let us know how it goes.

There is a very nice Le Meridien on the airport property as well as other hotels.