18 day Itinerary Advice: Hakodate/Tokyo/Hakone/Kyoto/Osaka

I’m arriving in Japan on May 1st and need some help in my planning. I’m aware I’m quite late to planning compared to most users here, particularly for the time of the year, but I’m not used to nailing down itineraries for my travels. Two of my main goals are to 1. catch the tail end of sakura season (meaning going north) and 2. spend a week or so in Tokyo, including a weekend. As it stands, the plan is to move from north to south. I’ve settled on a JR Pass to cover the entirety of my trip. Where I need help: 1. I have a couple of days yet to fill over my first weekend. 2. would like to hear opinions on whether to stay in Osaka or Kyoto, or stay in each city separately. 3. if possible, opt for night trains/buses. If there’s a better way to organize my journey that I’m not seeing, please feel free to suggest it.

* **3/4 Day 1**
* 16:35 Arrival at Tokyo
* check in at hostel/capsule hotel
* **4/4 Day 2**
* Stroll around Tokyo
* Quick shopping for travel items
* **4/5 Day 3**
* leave baggage at coin locker
* 8:30 Take Shinkansen to Hakodate
* check in hostel
* Fort Goryokaku
* **4/6 – 4/7 Days 4-5**
* Mt. Hakodate
* I need help with these days. My original plan was to leave for Hakodate on 4/4, and keep going north to Sapporo on 5/4, plan a day trip to Otaru while there and return to Tokyo on 8/4, but 8 hours of travel time is a waste of time and a plane ticket would be an additional cost on top of the $465 JR Pass. I don’t think I want to spend all the weekend of Hakodate either. I’d like to hear suggestions between Hakodate and Tokyo.
* **4/8 Day 6**
* train back to Tokyo
* check in hostel
* **4/8 – 4/13 Days 6 through 11**
* no set plans to explore Tokyo leisurely and spontaneously
* POIs: Imperial Palace, Tokyo Tower, Asakusa, Ueno Park, Tokyo Big Sight just because
* Akihabara for pop culture and camera shopping
* Shibuya at night
* Harajuku/Shinjuku shopping
* possible day trip to Mt. Fuji
* **4/12 Day 12**
* train/bus ride to Hakone\*
* check in at onsen resort
* (\*originally planned on Nagoya but I don’t want to miss the opportunity to stay at an onsen ryokan)
* **4/13 Day 13**
* early trains/bus ride to Osaka\*
* check in at hostel
* (\*settling on Osaka for the time being)
* **4/13 – 4/17 Days 13 through 17**
* back and forth between Osaka and Kyoto
* POI Kyoto: Fushimi Inari Shrine, Kyomizudera, Higashiyama, Kyoto National Museum
* POI Osaka: Namba, Osaka Castle, National Art Museum, Minoo Park, Shinsekai?
* **4/18 Day 18**
* early Shinkansen to Tokyo
* last minute shopping and/or strolling
* depart at 16:20

I hope this itinerary is detailed enough to meet the rules. I apologize as itineraries are not my forte and that’s why I seek advice from more experience travelers.

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