Hi there,
I think in your position I would do the following:
Metro pass deals on arrival into Narita
Purchase one of either:
These will to cover getting into town and your first few days of metro travel in Tokyo at a discounted rate.
I think if you're going to be in Tokyo for more than a few days, the NEX + Suica is possibly a better choice. Bear in mind that as it's a limited prepaid card (rather than infinite use day pass) it very much depends on your travel plans - break out the calculator ;).
Note that you can also purchase discounted 1 or 2 day metro passes at Narita. A good choice for you could be the Keisei Skyliner + 2 day pass deal, supplemented with a further 2 day metro pass (¥980 for 2 days) to take you up to the end of day 4. Please note that these discounted passes can only be purchased at Narita airport.
If you go to Mt Fuji
I recommend looking into Hakone for an overnight stay. You can purchase the 2 day Odakyu Hakone Free Pass for departure from Shinjuku in Tokyo for this.
JR Pass activation on day 5-11
Activate your JR Pass on day 5 for your trip down to Kyoto, travel to Nara and the region and then back up to Narita.
Hope this helps!
