Here are some of our favorite Japan travel recommendations

Kawagoe: Tokyo old city:
http://en.japantravel.com/saitama/a-day-in-kawagoe-saitama/6928

Expensive High End Restaurant:
https://tabelog.com/en/tokyo/A1301/A130103/13015849/

Less Expensive but Michelin recommended.  All fish shipped directly from Shikoku each day http://gm.gnavi.co.jp/shop/0117017301/

Tokyo Tours:
http://en.japantravel.com/tours/all/tokyo

Tokyo Tours:
http://www.japanican.com/en/tour/#map_kanto

One Day trip from Tokyo:Kamakura
http://www.japan-guide.com/e/e2166.html

Tokyo Fun Restaurant:
https://restaurants-guide.tokyo/restaurants/detail/50/

Shopping: Harujuku:
http://www.japan-guide.com/e/e3006.html

Shibuya:
http://www.japan-guide.com/e/e3007.html

Nice shop in Ginza:
http://www.akomeya.jp/shop/ginza.php

My favorite walking tour:
http://www.frommers.com/destinations/tokyo/walking-tours/walking-tour-4

Good soba place on walking tour https://tabelog.com/en/tokyo/A1310/A131004/13008456/

Also you have to go to this Tai Yaki place.  Mondale’s favorite place in Tokyo  https://tabelog.com/en/tokyo/A1311/A131106/13003570/

http://www.travel-around-japan.com/k31-50-yanaka-nezu-sendagi.html

Tokyo Nightlife

Shinjuku Ni-Chome

https://toyokeizai.net/articles/-/211787?display=b

https://www.jnto.go.jp/eng/spot/handcrft/kiyomizuyakipotterycomplex.html

NY Times suggestions for 36 Hours in Tokyo
It would not be the tour I would give. A bit too Shi-Shi for me. But has some good suggestions.
https://www.nytimes.com/interactive/2017/04/27/travel/what-to-do-36-hours-in-tokyo-japan.html?rref=collection%2Fsectioncollection%2Ftravel&action=click&contentCollection=travel&region=rank&module=package&version=highlights&contentPlacement=5&pgtype=sectionfront&_r=0

In Kyoto:
Kiyomizu Pottery Village: About 40 minutes from downtown. It used to be you could call and arrange to visit studios. Not sure if its still possible.
https://www.jnto.go.jp/eng/spot/handcrft/kiyomizuyakipotterycomplex.html

Restaurant where I used to work:
https://www.tripadvisor.com/Restaurant_Review-g298564-d1594953-Reviews-Kushihachi_Hakubai_cho_Main_branch-Kyoto_Kyoto_Prefecture_Kinki.html

This is a very interesting low cost housing alternative in Kyoto.  Not sure where its going to go from here (June, 2017) but worth considering.

http://mailman.japaninc.com/pipermail/terrie/2017/000503.html