We left on Saturday from LAX at 3:45 p.m. and arrived at 7:15 p.m. on Sunday @ Narita Int’l. We were able to go through Customs, pick up our luggage, exchange our Traveler’s checks, exchange our rail passes, make all of our seat reservations on the shinkansen (bullet train) and buy a Suica card (subway pass) by 8:15 p.m. It helped that Narita seemed pretty empty and that there was a person who spoke very good English in the Japan Rail (“JR”) office. Tip: don’t forget to fill out the back of the Customs cards…oops.
D used the bathroom at Narita and was confused by the setup. I didn’t see the facilities, but apparently he almost went in the sink!
The Narita Express was only running about once an hour, and only in the morning and night in order to conserve power. Luckily, there was a train that left at 8:45. 
You can use the JR Pass to get on the Narita Express. We were told all the seats were reserved (make the reservations in the JR office) but I’m not sure why, considering we almost had a whole car to ourselves! The train feels very new, and was a conveient way to get to the city.
We arrived at Tokyo station and had to transfer to the subway. We tried to swipe our subway card at the turnstile, not realizing that we just had to show our JR pass to exit. The subway card wouldn’t let us out (since it didn’t let us in) and we each tried to swipe it about five times before we figured it out. After that, it was smooth sailing, transportation-wise, which I was worried about. Even though the stations are huge, there is good signage everywhere (in English). The hyperdia website really helped us in planning all of our transportation routes.
We found our hotel in Akasaka and checked in around 10:15 p.m. 
The room was small, but clean and in a good location. However, we can’t recommend it, for a reason which we will discuss later.
D had a hard time sleeping due to the time change. I managed a little more sleep, but we both felt an aftershock around 2 a.m. It was very small, but a bit unnerving at the same time. (We felt another small aftershock the next night at around the same time).
We received breakfast coupons for the Excelsior Cafe attached to the hotel. The breakfast options were interesting, more like lunch to us. Sandwiches, or soup or hardboiled egg/toast, all accompanied by a green salad and coffee, tea or juice. 
D and I both chose the first option, a sandwich with egg salad, tuna salad and shrimp…yes, all three! We observed many men in suits drop by the cafe for their breakfast on their way to work. Also, we inadvertently sat in the smoking section and had to move to get some fresh air. Living in CA, we forget that people still smoke while they eat–gross. Fueled up, we were ready for our first full day by 7:15 a.m.!