More JR & Train Questions

Going to purchase a JR Pass in the next few days for two of us but probably not activate it till 12/2 because we will need it for more than 7 days but 14 is way too much. Our itinerary is Tokyo to Kyoto, Kyoto to Kinosakionsen, Kinosakionsen to Lake Kawaguchiko and Lake Kawaguchiko back to Tokyo to fly home. This will be done over about 13 days. I have noticed JR is running a lot more Nozomi trains and I know we can't ride the Nozomi and another train with our JR Pass. Having never been to Japan i Have the following questions:

1) How do we know the difference between a Nozomi train and say a Hikari which we can ride?

2) How do we know the Green Car section from the regular car section?

3) Since we are going in the middle of Koyo season in Tokyo-Kyoto-Kinosakionsen, will we have a problem getting a Seat Reservation once we are in Japan turning in our voucher for a pass? If you use a ticket from a ticket machine is there any issue getting a reserved seat say Tokyo to Kyoto?

4) What happens if you miss the train your scheduled on with a JR Pass because you get lost as I hear people sometimes do?

5) Would you choose JTB or Klook to buy a JR Pass here in the US since I need the 90 day window given I want to purchase at Today's prices but won't travel until November. (i know we cant book reservations online this way)

We plan to just buy two tickets from a ticket machine to get from Tokyo to Kyoto so we don't have to active our JR Pass and then wait until our last day in Kyoto 12/2 to activate it which means I won't get full value or all 7 days out it but it seems the JR Pass is just the easiest way to ride trains to me.

1) How do we know the difference between a Nozomi train and say a Hikari which we can ride?
2) How do we know the Green Car section from the regular car section?

Through signs in the station, on the platform and on the trains. Read on the basics here:
https://www.japan-guide.com/e/e2016.html
https://www.japan-guide.com/e/e2018.html

3) Since we are going in the middle of Koyo season in Tokyo-Kyoto-Kinosakionsen, will we have a problem getting a Seat Reservation once we are in Japan turning in our voucher for a pass? If you use a ticket from a ticket machine is there any issue getting a reserved seat say Tokyo to Kyoto?

The risk is generally low, especially if you reserve at least a day in advance.

4) What happens if you miss the train your scheduled on with a JR Pass because you get lost as I hear people sometimes do?

Your seat will remain empty and JR won't be able to sell it to somebody else, unless you cancel it in time. If that happens too often, the time will eventually come when JR disontinues the free seat-reservation priviledge.

5) Would you choose JTB or Klook to buy a JR Pass here in the US since I need the 90 day window given I want to purchase at Today's prices but won't travel until November. (i know we cant book reservations online this way)

I would chose neither, but the following service, because I know they work hard to try to provide a good service:
https://www.japan-guide.com/link.html?/e/e2361.html+text+experience+4+...

Are you 100% sure the JRP pays off for your trip? You are saying you will buy the 7 day (consecutive days!!!) version but your trip is 13 days and going from Tokyo through Kyoto to Kinosakionsen and then back to the Tokyo area. If your pass expires midway through, it will most likely not pay off.

Perhaps I was not totally clear. Yes a 7 day pass will be close to paying off because the first 5 days will be in tokyo but we will not use the pass thus not activate it. While there we will take a day trip to Nikko without activating the JR Pass. We then get a ticket from a ticket machine to Kyoto and spend 4 days there. The last day in Kyoto we will activate the JR pass so we can use it to get to Kinosakionsen on a limited express train and stay there 2 days. After our stay there we will head to Lake Kawaguchiko where we will ride a JR Train to Mishima and then get off and take a Non JR bus. We will be there for 2 days before heading back to Tokyo at staying at a hotel at Haneda so we can be ready for our flight the next morning. While the JR pass doesn't totally pay off, it is fairly close even though we are going to take the green car and will only get 6 days of use. I just want to be 100% sure we can get reserved seats because I am told since I will use a 3rd party we cannot book them online.

choose JTB. there should be no problem.
others are unknow third companies.

adjustment is rather complicated.
you can buy regular tickets.
on day1, from Kinosaki to Mishima (through Kyoto, not going out from Kyoto station) ,
stay 2 days around Kawaguch lake
on day3, go to Tokyo.
you can buy a single basic fare from Kinosaki to Tokyo, it is valid for 4 days.
buy a limited express ticket from Kinosaki to Kyoto and a shinkasen limited express ticket from Kyoto to Mishima, SIMULTANIOUSLY. you may get some discount, probably a half price, for the former express ticket. get out from Mishima station with HOLDING the basic fare ticket (from Kinosaki to Tokyo). you can go Kawaguchiko area. you buy a shinkansen express ticket from Mishima to Tokyo. (you already have the basic fare ticket. ) when you go out from Tokyo shinkansen gate, you again can receive the basic fare ticket from gate machine. the resulting basic fare ticket may be valid until you go out from JR stations in Tokyo ward area.

Ken,

Sorry I am not exactly clear on what you are saying below having never been to Japan and only to countries where 1 train line existed and 1 pass got us everywhere we wanted to go. We just feel that the JR Pass is the easiest way for us though it may not pay off 100%. We do not understand the Japan train ticket machine system and seat reservations. Please excuse my ignorance. Can you explain what you said bleow as I don't understand the discounts and basic fare ticket portions:

You can buy a single basic fare from Kinosaki to Tokyo, it is valid for 4 days.
buy a limited express ticket from Kinosaki to Kyoto and a shinkasen limited express ticket from Kyoto to Mishima, SIMULTANIOUSLY. you may get some discount, probably a half price, for the former express ticket. get out from Mishima station with HOLDING the basic fare ticket (from Kinosaki to Tokyo). you can go Kawaguchiko area. you buy a shinkansen express ticket from Mishima to Tokyo. (you already have the basic fare ticket. ) when you go out from Tokyo shinkansen gate, you again can receive the basic fare ticket from gate machine. the resulting basic fare ticket may be valid until you go out from JR stations in Tokyo ward area.

My questions is Would my JR Pass not cover Kyoto to Kinosakionsen and the Kinosakionsen to Mishima where we would then need to buy a Non JR Bus ticket? After we stay for two days at Lake Kawaguchiko do we have a JR Train option to get us back to Haneda in Tokyo? Yes we want to ride a Shinkansen Green car when ever possible.

your plan is that you buy a round trip from Tokyo to Nikko and one way from Tokyo to Kyoto separately from the pass. you use your JR pass in the route, Kyoto - Kinosaki - Kyoto - Mishima - Tokyo.
this usage may not be cost effective.
I have explained you an alternative idea that you buy regular tickets and use them a route, Kinosaki -Kyoto-Mishima-Tokyo, instead of using the pass. "regular" means "not the pass", normal.

of course, the pass has advantages other than the price. so that, it is your preference.

You're saying that the rail system is too complicated and want to buy a JR pass for convenience, even if it is more expensive than buying point to point tickets. On the other hand you are going to buy tickets from Tokyo to Kyoto...

You won't be able to use the website for reservations, with a JR pass bought through a 3rd party. Booking seats with a JR pass is just as difficult (or easy) as buying them without a pass, so you're not making your life easier with a pass.

If the main use of your pass is to go to kinosaki onsen, the Kansai wide area pass is cheaper.

While the JR pass doesn't totally pay off, it is fairly close even though we are going to take the green car and will only get 6 days of use. I just want to be 100% sure we can get reserved seats because I am told since I will use a 3rd party we cannot book them online
Don't buy the pass - too expensive, fewer trains, more transfers. You are not even using the pass for the round-trip! You know the Green pass is more expensive (not everyone realizes that).
Just get individual tickets, book/reserve online in advance - simple.