Or, if you wanted to get at least an hour's more sleep but still stay in Tokyo, find a place to stay in Ueno, take the 6:50 Keisei Skyliner, and get to NRT at 7:39 (still plenty of time for a 9:30 flight).

I'm not sure what OP means by "Tokyo-wide pass to cover the cost of the JR train to the airport." If OP means the Suica card (pre-paid card that can be used for Tokyo subway and local trains), then yes, the Suica can be used for the Keisei Skyliner.