1st time Japan trip - 14 days - Need advices

Good day from Perth, Western Australia

Hoping to get advices and suggestions from japan travel guru in this forum.

We're a family of 4 with 10yo and 6yo visiting japan for the first time from 1st Jan 2017 ( Narita ) and leaving on 14th Jan 2017 ( Kansai ). Dad is a foodie and Mum is bargain shopping hunter. We're on medium budget.

Our rough itinerary is as below
1st - Narita - Yuzawa ( staying at an apt in NAEBA )
2nd - Yuzawa ( Naeba n Kagura )
3rd - Yuzawa - Tokyo
4th - Tokyo DisneyLand
5th - Tokyo Disneysea
6th - Day Trip Fuji Five Lakes ( Kawaguchiko / Fuji Subaru 5th Station )
7th - Day Trip Hakone ( Hakone Loop )
8th - dont know yet
9th - Tokyo - Kyoto
10th - Suggestions on what to do in Kyoto?
11th - Kyoto - Osaka ( suggested activities in the morning in Kyoto and Afternoon in Osaka )
12th - Universal Studio ( maybe )
13th - Suggestions on what to do in Osaka?
14th - Osaka - Kansai International

Questions
1. On 1st, we will check in around 2PM. What activities available after this time? I read all ski resorts close at 5pm. We dont ski/board. Maybe kids want to take lesson.
2. We will buy the JR Tokyo Wide Pass for our first 3 days. Is this a wise move?
3. On 3rd, we will arrive in Tokyo in the afternoon. Suggested activities after checking in?
4. On 6th and 7th, i couldnt figure out the best value transportation for both places. Fuji Hakone Pass / JR Tokyo Wide / Bus / rent a car since there are 4 of us?
5. I am happy to pay a fee for someone to create itinerary for me. Can you suggest anyone?

Thanking you in advance.

Most things in Japan are closed from 1st to the 3rd for the New Year. As you'll be at a ski resort I imagine things there would be open, but don't expect there to be many shops / restaurants open on your way there, the same applies for your check-in to Tokyo on the 3rd.

As for the trip to the 5th Station on Mt Fuji, the bus route here will probably be closed due to snow. There isn't really much to do in Fuji Five Lakes except for seeing the mountain itself, which is often obscured from the observatory point if there's rain or cloud. There's a theme park there but it's often closed especially in the winter season. I would advise scrapping Fuji Five Lakes from your itinerary as you're going there off season when most things will be closed.

I think you should see the historic temples of Kyoto, and maybe do a day trip from Osaka to Nara to see the deer.

I don't think you need a JR Tokyo Wide pass on your first three days as you will be outside of Tokyo (Yuzawa).

You're not spending a lot of time in Tokyo itself - just one day, as far as I can tell. There's a lot to see in the city, so I'd suggest dropping one day trip or one Disney trip (Disneyland is much like other Disney parks; DisneySea is the unique one) so you can spend some time in the city. Even one day (the 8th) won't be enough!

For Kyoto and Osaka suggestions, read the respective sections of this website about each city.

1. Not sure, no personal experience, sorry.

2. As the first reply says, the pass may not pay off. You can use Hyperdia (hyperdia.com/en) to calculate fares to see if you would get value from the pass.

3. What area are you staying in? Again, check the Tokyo section of this website for ideas.

4. For Hakone, get the Hakone FreePass; it covers a return trip to Hakone from Shinjuku Station, plus all the transport for the Round Course (and some extra discounts).

5. A travel agent.

G'day mate; welcome to the freezing cold northern hemisphere. 4 and 6 yo; brave pair aint ye!
Seriously: try the Zoo in Ueno Park, Tokyo. BTW, try to do something with your plans so you aren't wasting most of the daylight hours on the train. To continue: Pick one Disney Park, my daughter swears that Tokyo Disney is worth it even if you've been to a Disney Park. I think your kids will like either the Tokyo Skytree or the old "Godzilla-y" Tokyo Tower with One-Piece manga attraction included. They will like Universal Japan in Osaka. Heck, they may like the Kyoto Tower too and it's close to the train station. Do Hakone, skip the frozen tundra of Fujifivelake this time of year. And check this site for ninja and martial arts shows; all kids like that stuff. As for you and the missus, "foodie....bargain shopper" you've going to heaven! Enjoy.

Coldest and snowest period of the year. You may get held up inside for a day. I would just have a list of things to do, and not stick to too much of a plan and cross things off your list as you go.

For ideas of what to do. Just look at this website. Get your family in front of the computer and start clicking. Your family will find many things to do. Clearly some aren't available to you due to the season, but still plenty of things to do.

Thank you to all who had given your advices.

Re-thinking our plan now and hoping for more suggestions.

So you're rethinking this section:
6th - Day Trip Fuji Five Lakes ( Kawaguchiko / Fuji Subaru 5th Station )
7th - Day Trip Hakone ( Hakone Loop )
8th - dont know yet
9th - Tokyo - Kyoto
10th - Suggestions on what to do in Kyoto?
11th - Kyoto - Osaka ( suggested activities in the morning in Kyoto and Afternoon in Osaka )
12th - Universal Studio ( maybe )
13th - Suggestions on what to do in Osaka?

Without changing any hotel reservations you may have, you might want to look at some of these ideas. I haven't been to Kyoto and Osaka yet so I don't have any child-friendly ideas there.
6th - Tokyo - Odaibah - plenty of shopping there plus the Trick Art Museum, Joypolis, and Miraikan, the Science Museum.
7th - Day Trip Kamakura? Or Zojo-ji and Tokyo Tower? Or back to Odaibah for what you didn't see yesterday?
8th - Ueno - zoo and National Museum of Nature and Science
9th - Tokyo - Kyoto. Maybe take the children to the nearest park or gardens before the train ride so they can run around a bit.

OP, as a fellow Australian I don't recommend Ueno Zoo. It's very different to zoos in Australia; a lot of concrete, not much effort to create more natural environments for the animals. It might be a bit depressing.