Order of Itinerary in Tokyo

Hi,
Yes, you can use the JR Pass on the Yamanote Line. If the order of your activities is not important, why not use the pass all you can?
For Tsukiji, you need to get there early in the morning (actually about 4 AM if you want to be on one of the tours). After 9 AM things wind down pretty quickly. It may be better to get a good night's sleep before you have to take your flight, so seeing Tsukiji on a different day may be better.

For the N'Ex, yes you need to make seat reservations going back. As for 'best', it's unclear how you define it. It is quick and convenient, but not the cheapest way. If you'd like to save about ¥2000 yen per person, there is the ¥1000 yen bus from Tokyo Station. Choose which you prefer.

Good luck.

The ¥1000 yen bus is a great option, but when I googled, our hotel is 18km away from the bus stop. The cab ride from our hotel to Ginza Station is ¥2500 taxi.

Could we use the JR pass to travel to Asakusa and Odaiba?

Hi,
There is no JR access to Odaiba.
Your other issue I don't understand - you can easily take the Yamanote Line from Shinjuku to Tokyo Stn to get the ¥1000 yen bus. I suggest you google "Yamanote line map" and get familiar with it. For Asakusa, you can take the Yamanote Line to Ueno, and then take a subway 3 stops to Asakusa. If you want to see the Sensoji Temple, it is very close.

Best of luck.

We will have luggage with us so I am afraid we will take up too much room on the train. Will the Yamanote Line be busy on Saturday around noon?

Certainly not as much during weekdays, especially rush hour. Most stations have lockers you can use, and if you like, there are some takuhaibin services you can use to deliver your bags to a future place and time, or even the airport if you like.

Also, for Harajuku, the best time to go if you are flexible is on a Sunday afternoon. The girls with the wild fashions are really something else. There is also Meiji Shrine and Yoyogi Park close by, and the famous Takeshita St. for shopping.