This will seem strange, since I started the Skyliner idea in the first place, but you might want to think about it some more. I just noticed your planned arrival time. A 3:30 pm arrival at NRT will put you on the train around 4:30 and arriving at Ueno some time around 5:30 - 6:00 pm or so. The rush hour will be in full swing and subways will be very difficult if you have much luggage OR if you aren't familiar with where you are going and how to get there. In this particular case, the N'EX or even the airport Limousine Bus might be worth considering.

Just a little something to confuse you even more.

JR