Train Tickets for 2 days in Tokyo

Hello,

As planned, our JR Pass will expire on Dec04, but I will Tokyo on Dec06 late pm. I still need transportation for some sightseeing on 1 and 1/2 days in Tokyo.

Are there some daily JR passes for local trains if my trip includes buses as well?
I've read about the discounted tickets, such at the Seishun 18 Kippu and other seasonal discounts.
On one of those trips on the 5th I have to transfer hotels and travel with luggage.

Thank you!
Elsa