Stay near Sangen-Jaya or Nippori

Hi!
I'm planning a trip to Japan on Nov 26 - Dec 2, 2017. I'm currently looking for accommodation near Sangen-Jaya and Nippori Station. I have some questions:
1. I've been looking into some day passes but I don't think there is one that covers sangen-jaya, is that correct? If I buy Tokyo Metro 24 Hours Ticket, how does it work getting on and off Sangen-Jaya Station? For example I want to go from Oshiage to Sangen-Jaya, do I need to get out from Shibuya station with Tokyo Metro 24 Hours Ticket and tap in with pasmo card or do I just pay the additional fare at Sangen-Jaya Station?

2. If I choose to stay near Nippori Station, I'm thinking of buying Tokunai Pass. But the pass does not cover travel to Mitaka (Ghibli Museum) and Maihama (Disneyland). Again, should I get out from the last station covered by the pass and come back in again or can I just pay the additional fare at my destination station?

3. I'm going to arrive on nov 26 around 2 PM at Narita. I think I will take Keisei Sky Access Express at 4.30 PM, after immigration and all. Will that train be full at that time? I will transit at Oshiage Station and take another train to Nagatacho (Hanzoman Line to Chuo Rinkan), will I be stuck at rush hour then? I travel with my husband and 3 yo son.

4. I'm a bit confused with Disneyland cutoff age for child. My son will be 3 years and 3 months old when we visit, is it still free admission for him to Disneyland?

5. What to be expected, weather and temperature wise, from visit to Karuizawa ski resort and Kawaguchiko in late november?

6. What is the weather and temperature like in Tokyo in late november?

I think that's all for now. Thank you for your help!

When your departure station in within a pass's coverage area and your arrival station is without, you enter the departure station with (only) your pass, and at the arrival station you show your pass to an attendant, who will ask you to pay the fare for the section not covered by the pass and then let you exit.

In the opposite case, buy a paper ticket to cover the section not covered by the pass, and use the ticket to enter and the pass to exit. The ticket will not be collected but that doesn't matter; throw it away or keep it as a souvenir.

Note that in both cases you can't use IC cards; if you want to use one you must exit and reenter at the boundary station.

Hi Firas, thanks much! That's very helpful.

I have another question regarding Karuizawa ski resort. If I dont intend to play ski, can I not purchase ski lift ticket but still be able to enter ski/snow area? I just want to play at kids area, sliding and tubing with my son.

Thanks.

In the first case it may also be possible to buy the ticket for the non-pass-covered section in advance. With JR you can do it at any ticket office, but typically not at ticket machines. Not sure about other companies.