Japan Trip Tentative Schedule

I'm planning to buy JR Pass prior to my Japan trip, this pass cost quite a bomb (¥ 28,300), yet I believe it will be worthwhile, especially if I'm taking shinkansen Tokyo <-> Kyoto.

There's so many places I want to visit in Japan, but due to the time constraint, my main priority for this trip is to visit iconic places in Japan, including sites that are under UNESCO World Heritage list (marked as UNESCO below).
Anyway, here's the tentative schedule, let's see how much of these we can cover :p

Fri, Jan 30
21:00 Take cab to Changi Airport
21:30 Check-in & shop for gifts
23:00 Boarding
23:45 Depart from Changi Airport Terminal 3 - SQ638

Sat, Jan 31
07:15 Reach Narita Airport Terminal 1 -> Immigration
07:45 Buy NEX&SUICA package (¥ 3,500)
08:11 Take Narita Express (NEX) from Narita Terminal 1 stn to Yokohama stn
09:59 Reach Yokohama stn, drop luggage at Yokohama Tokyu Excel Hotel & take JR Yokohama Line - Negishi Line to Shin Yokohama stn
10:52 Take Hikari Shinkansen from Shin Yokohama stn to Kyoto stn
13:16 Reach Kyoto stn, buy 1 or 2 days city bus pass (¥ 500 per day)
14:00 Walk to Toji Temple (¥ 500 - UNESCO)
15:00 Walk to Honganji Temples (Nishi & Higashi Honganji - UNESCO) -> Kawaramachi Catholic Church
19:30 Check-in to Tomato Guest House (¥ 2,900 per person per night)
20:30 Meet wifey at Kyoto Station -> Kyoto Tower (¥ 770 - Observatory entrance is optional)

Sun, Feb 01
05:00 Breakfast
05:33 Take bus 206 from Kyoto stn to Gojozaka -> Kiyomizudera (¥ 300 - UNESCO)
07:00 Walk to Yasaka Pagoda (another link) -> Ryozen Kannon
08:00 Walk thru bamboo pathway to Kodaiji (English link - ¥ 600) & Entoku-in (optional)
09:00 Walk to Ishibe Koji Street
09:30 Walk to Yasaka Shrine (another link) -> Maruyama Park
10:30 Walk to Chion-in (¥ 400)-> Shoren-in (optional) -> Heian Shrine (optional)
12:00 Walk to Nanzenji (¥ 500) & Konchi-in (optional)
13:00 Walk to Eikando Temple (optional) -> Nyakuoji (optional)
14:00 Walk to Anraku-ji (¥ 300) -> Honen-in -> Ginkakuji (¥ 500 - UNESCO, we heard that the main temple is under renovation...)
15:34 Take bus 102 from Ginkakuji-michi stn, change at Horikawa-Imadegawa stn to bus 101 to Nijojyo-mae stn -> Nijo Castle (¥ 600 - UNESCO).
De-tour to Kyoto Imperial Park is also possible if time allows.
17:00 Take bus 12 from Nijojyo-mae stn to Shijo-Kawaramachi stn (Downtown Kyoto)
18:30 Attend the Sunday Mass at Kawaramachi Catholic Church
19:30 Walk to Gion
21:00 Take bus 206 back to Kyoto stn.

Mon, Feb 02
05:15 Check-out from Tomato Guest House
05:43 Take bus 南５ from Kyoto stn to Fushimi-Inari-Taisha Shrine (UNESCO)
09:00 Take JR train from Inari stn to Saga Arashiyama stn -> Tenryuji (¥ 500 - UNESCO) -> Bamboo forest -> Sagano
10:00 Take Subway from Arashiyama stn to Omuro Ninnaji stn -> Ninnaji (¥ 500 - UNESCO) -> Ryoanji (¥ 500 - UNESCO, we heard it's closed from Jan 5 - Feb 5, crossing fingers...)
11:00 Walk to Toji-in (Optional) -> Ritsumeikan Uni (Optional) -> Waratenjin (Optional)
12:00 Walk to Kinkakuji Temple (¥ 400 - UNESCO)
12:58 Take bus 102 from Kinkakuji-michi stn to Karasuma Imadegawa stn
13:45 Tour Kyoto Imperial Palace
15:30 Take Subway from Imadegawa stn to Kyoto stn
15:56 Take Hikari Shinkansen from Kyoto stn to Tokyo stn
18:40 Reached Tokyo stn, change to JR train to Ryogoku stn/continue to Ueno stn then change to Ginza line subway to Asakusa stn -> walk and check-in to Khaosan Hostel Annex (¥ 1,500 per person per night, excl booking fee ¥ 200)
19:30 Explore Ginza/Tokyo Tower

Tue, Feb 03
04:30 Breakfast
05:30 Take Ginza line subway to Ginza stn -> Walk to Tsukiji Fish Market (maybe cannot as subway start later...)
06:30 Walk to Hama Rikyu Garden (¥ 300)
08:30 Walk to Sengakuji
11:00 Take Asakusa line subway to Higashi Ginza stn then change to Hibiya line subway to Nishi-Arai Daishimae stn -> Nishi-Arai Daishi (Daruma Kuyo Festival)
12:30 Take Hibiya line subway to Ueno stn then change to Ginza line to Asakusa stn -> Nakamise-dori -> Sensoji (Setsubun-e Festival)
14:30 Akihabara (depends on Setsubun-e festival schedule)
16:00 Asakusa take Ginza line subway to Ueno stn -> Ueno Park
18:00 Take JR line from Ueno stn to Hamamatsucho stn -> walk to Roppongi Hills
19:00 Take JR line from Hamamatsucho stn to Shinjuku stn -> Shinjuku
20:00 HardRock Cafe

Wed, Feb 04
07:00 Shibuya -> Harajuku
08:30 Explore Imperial Palace East Garden
09:45 Imperial Palace (Booking required)
11:30 Take JR Yokosuka Line (Track 1,2,3) from Tokyo stn to Kitakamakura stn, take photo of Ofuna Kan'non (Kamakura visit might be separated into 2 days if not enough time)
12:30 Reached Kitakamakura stn -> Engakuji (¥ 300) -> Tokeiji (Optional) -> Jochiji (¥ 200) -> Meigetsu-in (Optional) -> Chojuji -> Kencho-ji (¥ 300) -> En'noji (Optional)
14:30 Walk to Tsurugaoka Hachimangu Shrine (¥ 100) -> Jyomyoji (¥ 100) -> Jyufukuji -> Myoryuji -> Daigyoji -> Kamakura stn
16:00 Take JR train from Kamakura to Hase stn then walk to Hasedera & Benten-kutsu Cave (¥ 300) -> Kotoku-in & Daibutsu (¥ 200)
17:30 Walk to Kamakura stn
18:00 Take JR Yokosuka line from Kamakura stn to Yokohama stn
19:00 Check-in to Yokohama Tokyu Excel Hotel
21:00 Minato Mirai -> Queen's Tower (HardRock Cafe) -> Cosmo Clock -> Nippon Maru

Thu, Feb 05
08:15 Meet Hayashi-san at Hotel lobby
09:00 Training in Hitachi Software Division - Totsuka
18:00 Dinner
21:00 Red Brick Warehouse -> Yokohama Bay Bridge -> Chinatown

Fri, Feb 06
09:00 Training in Hitachi Software Division - Totsuka
12:00 Lunch
13:00 R&R in Yokohama (Landmark Tower -> Yamashita Park -> Marine Tower -> Harbor View Park) or continue to Kamakura

Sat, Feb 07
08:00 Check-out from Yokohama Tokyu Excel Hotel
09:00 R&R in Yokohama (Landmark Tower -> Yamashita Park -> Marine Tower -> Harbor View Park)
15:30 Take Narita Express (¥ 4,180) from Yokohama stn to Narita Terminal 1 stn
16:59 Reach Narita Terminal 1 stn & check-in
18:00 Boarding
19:00 Depart from Narita Terminal 1 - SQ11

Sun, Feb 08
01:25 Reach Changi Airport Terminal 1