I don't think you can cover so many places. I went to Osaka & Kyoto last Feb. 10 days 9 nights also not enough cover.
heres mine back in feb.

Places of visit in sequence:
- Kyoto
- Hiroshima & Miyajima
- Tokyo
- Takayama (Gifu)
- Nara
- Koyasan (Wakayama)
- Osaka
Day1 - Kyoto
Touch down in Kyoto in the evening. But since its Sunday, theres only few imigration counter opened. Stuck there over an hour. By the time exited the airport, its already sunset. Weather was good, but it took 1hrs+ from KIX to Kyoto. Since i felt kind of tired, I didnt go out to Gion that night. MAJOR mistake made as weekends at Gion should be happening.
Day2 - Kyoto
Morning started cloudy. By the time I cleared Nijo Castle,iIt rains. Basically all my walk-on-foot-travel in central area Kyoto was kind of fail scenery.
Day3 - Kyoto
Rain the whole day till late evening. My Arashiyama trip was FAIL as well. God of Kansai must hate me so much for some reason.
Day4 - Hiroshima.
Activated my JR pass n hop on the Shinkansen to Hiroshima. Weather was somehow sunny morning in Kyoto. FFFFFFUUUUUUUUUUUUUUU. Best troll.Once Arrived in Hiroshima, walked around the central area at the memorials.
Day5 - Hiroshima
Morning started a lil cloudy. Off to Mazda muzeum but I missed the factory tour session. Afternoon in Bishamondai hills for panorama shots. Got lost there, but some elementary schooler helped me out

Evening in Miyajima island
Day6 - Hiroshima/Tokyo
Its a Friday, n odd to Higashi Hiroshima for Friday prayers. Met some new malaysian friends who brought me to mosque, n drive me out at higashi areas. Later in the evening, off to Tokyo. Had to switch shinkansen at shin-osaka for Tokyo. Shinkansen journey of 1000km. Arrived 10pm+ in Tokyo. It snows
Day7 - Tokyo
Off to Toshimaen for a cosplay outing. Later in the evening, went to Shinjuku n nearby areas to scout for some 2nd hand camera gears
Day8 - Tokyo
Didnt feel well in the morning. Only got out hotel in the afternoo, heading to Akiba for some shopping.
Day9 - TakayamaOff to Takayama in the morning. Journey was 3hrs+. Reached the Alps. snow everywhere~
Day10 - Takayama
I disched my Shirakawago plans, n opted for Snowboarding session instead at Arkopia Ski Resort. Massive body ache at the end of the day. Took an evening departure to Osaka as today is my last day of using the JR-Pass
Day11 - Nara
Im actually based in Osaka, but Nara is just an hour trip on JR. Body somehow still aches, but I can still walk around in Nara for sightseeing. It rains in the evening =__=.
Day12 - Osaka
It rained the whole morning. Kansai God sure hate me much. Since weather forecast indicating Koyasan/Wakayama is raining too, decided to just laze around inDenDem/Nippombashi and Shinsaibashi.
Day13 - Koyasan
Weather was good today, off to Koyasan for a day trip. Unexpectedly kind of far and train is slow. loose lots of time, but worth the visit.
Day14 - Osaka
Rain somewhat the whole day today. Went to ATC-Osaka for Cosjam cosplay outing. Luckily its indoors. Nothing much else.
Day15 - Osaka
Packed my stuff, n had a short visit at Osaka Castle since its not raining today. Stopped by DenDen for my final weeaboo hauls. Off to the airport
Due to bad timing plans, I had to cancel my Shirakawago, Biwako and Ise stops.