I've been to Tokyo, Japan just recently and here's how my itinerary looked like:
Day 01: Arrival at Narita Airport
- Buy SUICA Card at the Keisei Liner
- Check the Schedule of Keisei Limited Express to Haneda
- Check which platform to go to
- Get off at Asakusa Station (fare I think is only JPY 1300)
Day 02: Tokyo Tour
- Tour the Imperial Palace
- Visit Tokyo Tower
- Visit Roppongi Hills
- Visit Shibuya Crossing
Day 03: Mt Fuji Tour
Day 04: Shopping
- Visit Akihabara
- Visit Harajuku
- Visit Yoyogi Park
This is how Narita Airport looks like:
The direction to the railways are prominently marked so you wont get lost.
From Narita Airport, I booked a room at Khaosan Inn Original and this is in Asakusa. Since it is very near Asakusa Station, it is just a small walk away. Just look for the red bridge, DO NOT cross the bridge since you gotta turn right, and walk for 3 minutes. You wont miss it from there.
From the hostel, it is an easy walking distance to Asakusa Temple and Tokyo Syktree.