Currently Itinerary i thinking of doing in Dec/Jan

Tokyo 1-9 (Hotel $713-$1,333)

Day #1.
-Arive in Narita Airport 17:30
Tokyo 1-9

-Train to Tokyo 16:00?
-Check into Hotel
-Find food

Day #2.
-Zoji-ji Temple (1hr) – Free
-Tokyo Tower (1-2hr) – $16-$35

Day #3
-Yoyogi Park (1-2hr) -Free
-Shinjuku Gyoen National Park (1-2hr)-$5.26

Day #3
-Imperial Palace -Free?
-Yusukuni-ninja Shrine -Free

Day#4
-Free day

Day #5
-Hie Shrine -Free
-Staring Garden – Free

Day #6
-Shibuya Crossing
-Bellovisto (Bar)
-Tokyo City View – Night

Day #7
– Nezu Shrine
-Akihabara Electric Town

Day #8
-Free Day

Nagano 9-12 (Hotel $648)

Day #9.        
(Hire car $532.23)
-Hire car (Tokyo – Nagano) (3-4hr)

Day #10
-Matsumoto-jo Castle (1-2hr)-$7.36

Day #11
-Nagano

Day #12 (Nagano-Tokyo) (7am-2pm)
-Chureito Pagoda (1hr)
-Fujinomiya (1hr)
Back to tokyo

Hiroshima 12-17 (Hotel $598)

Day #12 Tokyo – Hiroshima
(Bullet train $197.70)
(16:30-20:30)
-Check into Hotel

Day #13
-Atomic Bomb Dome – Free
-Hiroshima Memorial Hall – Free

Day #14
-Hiroshima Castle – $3.89
-Shakkeien Garden – $2.74

Day #15
-Hiroshima

Day #16
-Miyajima Island

Day #17 (Hiroshima-Himeji)
(Bullet Train $85.09)
(10:03-10:58

-Himeji Castle (2hr)

(Himeji – Osaka)
(Bullet Train $35.30)
(15:11-15:46)

Osaka 17-25 (Hotel $631 – $1,204)

-Check into Hotel

Day #18
-Osaka SkyBuilding
-Osaka

Day#19
-Osaka Peace Centre
-Museum Of History

Day #20
-Osaka Castle $6.24

Day #21
-Osaka Aquarium? $ 28.40

Day #22
-Arimaonson (Morning)
-Kobe (Afternoon)

Day #23
-Osaka/Day Off

Day #24
-Ikeda

Kyoto 25-33 (Hotel $716)

Day #25
-Osaka – Kyoto

Day #26
-Nara

Day #27
-Fushimi-Momoyama-Jo Castle $27.46
-Fushimi Inari Taisha -Free

Day #28
-kiyomizudera Zuigude

Day #29
-Kyoto

Day #30
-Kyoto (New Years)

Day #31
-Nijo Castle $8.42
-Toji Kyoto -Free

Day #32
-Kyoto Palace

Sapporo 33-38 (Hotel $568)

Day #33
-Kyoto – Sapporo ($449 Flight)

Day #34
-Sapporo
-Beer Museum

Day #35

Day #36

Day #37

Day #38
-Sapporo – Tokyo

-Flight Home.

Estimated cost
-Hotel $3,874 – $5067
-Car $532.23
-Attractions $168.52
-Flights $1,297
-Bullet Train $318.09
-Sapporo Flight $449

Total $6,638.84 – $7,831.84

A few things I haven't quiet looked at like a Suica card for Tokyo or if it's worth getting a JP Pass.