2 day in Tokyo with JR pass - need to buy a one-day pass in Tokyo?

Hi there

My family of 5 will be in Tokyo on 13 & 14 Dec. Here is our planned itinerary.

13 Dec - One-day Tokyo Disneyland
13 Dec - Check in to Toyoku-Inn Tokyo Tozai-Sen Nishi-Kasai
14 Dec - Visit Asakusa (Tokyo Skytree ?), Shibuya & Shinjuku
14 Dec - Leave for Osaka at 5pm via Shinkansen (see hyperdia route 3 with 2 transfers - Does JR pass cover the LTD thunderbolt 40? http://www.hyperdia.com/en/cgi/en/search.html?dep_node=TOKYO&arv_node=UNIVERSALCITY&via_node01=&via_node02=&via_node03=&year=2012&month=12&day=14&hour=17&minute=00&search_type=0&search_way=&transtime=undefined&sort=0&max_route=5&airplane=off&ship=off&sprnozomi=off&bus=off&walk=off&lmlimit=null&search_target=route&facility=reserved&sum_target=7)

Do we need to purchase any one-day pass in Tokyo for the above itinerary?

Hope to hear from you soon.

Thanks again!