Narita-Tokyo-Kyoto itinerary and transit help

So I need lots of help because technically on a budget but I have 2 finicky older adults (my mom and aunt). We also will have 2 large 23kg luggage. We arrive in Narita around 8:45pm on Nov 15th and leave on Nov 20th at 5pm (so 5 days).

The plan is to visit Kyoto for about 2 night and then back to Tokyo (I know it's expensive, but we were not able to fly into KIX so do we fly or train?) If we train, we planned on using the Japanican 3 days package with lodging (Why is Kyoto lodging so expensive? It's like 200+ wherever I look making the 26.4k yen per person including transportation very attractive)

Another problem I have is my arrival in Narita at 8:45pm. This requires taking local trains since NEX last train is at 9pm. The question is where to stay. If I fly from Narita to KIX, I can stay around Narita (if there's nothing to do in Tokyo at night). But if we're going into Tokyo that night(and where would it be convenient for night sights), it's pretty much a given we will be taking a train. But regardless of where we stay, what can do we do so late at night, thus is it worth it going into Tokyo that late? (Older adults so not interested in bars and such). Food might be an issue as well. I was thinking of Akasaka, Tsukiji, and Roppongi (all airbnb unless not recommended?)

If we forgo Tokyo, we can make side trips to Yokohama, Kamakura and Kusatsu would be the alternative (but they really want to go to Kyoto and see the leaves and shrines). Is that realistic (if this was plan B).

Thoughts? Here my tentative plan

11/15 - Night in Tokyo somewhere, look at Shinjuku? I think Tokyo Met building will be closed by the time we get there(that's pretty much all we can do I think)

11/16 Tsukiji market for breakfast than walk to Ginza, or detour to Tokyo SkyTree or Toranomon Hills?, train to Imperial East Gardens, then train Asakusa then ferry to Odaiba for the onsen attraction

11/17 (Assuming Train - 26.4k yen)
Explore surrounding area of hotel or go to Marunouchi Building ? (something close to Tokyo station that's open early)
-Leave Tokyo station for Kyoto at 10am-12pm (not sure what our ticket will say),

OR fly from Narita to KIX (12k yen) at 8am and then pay for 4000 ICOCO and Haruka pass get to Kyoto station (Oh hm, guess I don't save at all, but I get to Kyoto earlier and I guess I can extend being in Kyoto 1 day, but do I dare rely on low budget airlines the day of my international flight?)

Kyoto Day 1
arrive 1pm-3pm
Go to hotel and after checking in walk to Nishiki Market to look around(Karasuma Kyoto Hotel)

-Higashiyama District (taxi? bus? I know things might be closed, depending on how long we walk through the Nishiki market)
- Kiyomizudera since it's open for night illuminations at 6:30
-Gion walk around and dinner (taxi from Kiyomizudera)

Day 2
- Inari shrine (train) early 7:30am?
- Tokufiji temple (train)
- Sanjusangendo (train)
- Arashiyama (train? I have to go back to Kyoto station and take the JR I think)
-Kitano Tenmangu Shrine (night illuminations, and I think this is a train also?)

11/19 Go back to Tokyo get there around 2pm to 5pm - go to Yokohama? or stay a little long in Kyoto? I'm not sure how the Japanican package tickets work but I can't request an earlier time so I would be scared to leave on 11/20. I heard if you miss your train you can use the reserve seats for unreserved seats, which might work and we can stay an extra day in Kyoto.

11/20 ??? before leaving at 3pm to go to Narita airport for 5pm flight.

I did consider the Japan rail pass but considering we would only use it for the Tokyo - Kyoto portion and only are 3 days in Tokyo, I don't think we can make the most out of the pass. We could however, leave whenever we wanted from Kyoto. Any suggestions welcome.

I can't help with your itinerary, but regarding the JR Pass, a return trip from Tokyo to Kyoto (272k yen) almost covers the 7 day pass (about 290k yen). If that gives you more freedom, go for it. Budget airlines in Japan are mostly okay from what I've read (everything and everyone in Japan runs on time!), but if you wanted to fly I would suggest taking a morning flight just in case there is a delay.
Hotel prices in Kyoto are expensive for that time period because a) it's soon, so you've missed the early booking deals, b) places are starting to fill up, so the places that still have rooms can charge more, and c) it's autumn leaf season, so the area is very popular. You could try staying just outside of Kyoto instead. Don't go with AirBNB though; I did my initial search through them and it looked lower value. Plus, addresses in Japan are notoriously difficult, even for locals; I felt much more secure booking a hotel which gave me directions from the closest train stations and would probably be easier to find for taxis!

For 5 days trip, Kyoto trip from Tokyo is normally not advisable... but if you have/want to do it then ...

Kyoto lodging, what hotel did you book? Location and type of hotel normally affects the price, but Kyoto hotel is normally still within reasonable range as long it is NOT during peak season or holiday season.

Last NEX train is at 21:46, so you might be able to make it if you can clear the custom fast and get your ticket, otherwise you could just stay near the airport.

11/16 - way too packed, not possible to fit all them in, maybe if you start early at Tsukiji then Ginza then Asakusa then Odaiba (better if you have more time here, can totally spend a day in here) , something like that might work.

For round trip between Osaka/Kyoto and Tokyo, get a JR 7 days pass, they will pay off, JR 7 days pass is 29110 Yen. Assuming from Tokyo station to Kyoto station, the fare is 13400 Yen one trip, so 26800 Yen for 2 trip.

For plane do not forget to include the boarding time and clearance time as a total traveling time, probably better just take Shinkansen to Kyoto and back, after all taking Shinkansen is one of the experience in Japan especially for your first time.

Not too sure what is your Japanican package is, probably would be better if you provide the information for others to look at.

I still do not think it is advisable to go to this 2 towns in period of 5 days, if your ticket is not finalized and you still want to go to both. Could you book the ticket in such a way that you entry from Kansai Airport and leave from Narita? (or vice versa) this way you will save some times and your budget.

The Japanican package is this:
http://www.japanican.com/en/special/tours/shinkansen/index.aspx

It's 26.4k yen for the dates we are staying, which includes hotel and the shinkansen round trip fare from Kyoto and Tokyo.

Where would you recommend to stay in Kyoto, that is reasonably priced. All the dates I looked at were $200+ for a single and I need at least 2/3 rooms then. That's if we go with the JR pass instead of the Japanican package.

11/16 - We can skip Asakusa and Ginza then I suppose. I thought we could as they are not really interested in shopping so it's really just a pass through Ginza and Odaiba. So Tsukiji, Imperial East Gardens, [insert tall location here], and Odaiba then.

Hi,
I'll leave the costing to those who know better, but I think you need to consider.. Do I have a whirlwind tour of lots of places and remember very little, or do I choose less and enjoy the places and have great memories.
Since your flight comes in later in the evening I would stay near Narita in one of the airport hotels which do give good value for money, check agoda, or similar and take a LLC
flight to Kyoto early next morning. Since you are coming in on an international flight you and your family may well be tired and glad to rest the day you arrive.
You can leave your luggage at your intended hotel, even if you cannot check in and get down to the market. Maybe in the afternoon you could join a 1/2 day tour and take in various places. Buses leave outside the Kyoto Station.. search online .. You have another day for touring the next day and even 1/2day if you want before catching Shinkansen to Tokyo, and doing what you are interested in. As well consider hotels that offer triple beds in one room if you need to cut costs on accommodation. Japan seems to be fairly unique in this bed
style.

Sorry I meant to say take flight to KIX, not Kyoto.

Personally, I would do Tokyo first. Since time seems to be the biggest constraint here, I think going from Narita to Kyoto in the morning of the 16th would be a waste of time.

So I would do:

Book a hotel near Narita Airport, preferably one which offers a free shuttle bus to/from the airport which you can take around 10 pm. (International Garden Hotel Narita is a possibility, you can book it on booking.com.) Go there after your flight.

On the morning of the 16th, go to Tokyo.

Go to Kyoto on the evening of the 17th or 18th depending on how much time you plan to stay there. Unless you are on a very tight budget, take the Shinkansen, not a flight.

On the 20th, take Jetstar flight 204 (14:00-15:20) to NRT, this will leave you ample time to take your flight at 17:00.