QUOTE(royalz @ Dec 11 2017, 08:28 PM)
Hi guys, can provide some comments to improve on my itinerary below? Is it okay? Thank you in advance...will be travelling there 20 april till 2nd may next year.
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Day 1: Arrival at Narita Airport
• Morning afternoon : Meiji Shrine, Harajuku
• Evening night : Shibuya area: Shibuya-crossing, Hachiko statue
Day 2: Tokyo Kyoto (Day 1 of JR Pass)
Assuming depart at 8, reach Kyoto at 10 am.
• Morning afternoon: Kyoto Station’s Ramen Street, Fushimi Inari
• Afternoon: Nishiki Market
• Evening night:
Day 3: Kyoto (Day 2 of JR Pass)
• Morning Afternoon : Arashiyama District – Senryuji temple (Yukata), Tenryuji temple, bamboo groves, Nonomiya Shrine
• Afternoon: Kinkaku-ji (Closes at 5 pm)
Day 4: Kyoto (Day 3 of JR Pass)
• Morning afternoon: Hanamikoji Dori (Kimono, Geisha), Gion, Kiyomizu-Dera (like JiuFen)
• Others: Ginkakuji
• Can consider going to Osaka
Day 5: Osaka (Day 4 of JR Pass)
• Morning: Osaka Castle (optional)
• Afternoon night: Shinsaibashi, Dotonbori Nipponbashi Namba (Don Quijote, Donqi)
• Others: Shinsaibashi (Shopping), HEP Five mall, Ferris Wheel (near Umeda Sky Building), Pokémon Centre
Day 6: Osaka (Day 5 of JR Pass)
Whole day: Universal Studios
Day 7: Osaka Nara (Day 6 of JR Pass)
• Take Kitetsu line from Osaka
• Morning afternoon: Nara
• Afternoon night: see Others (Day 5)
Day 8: Osaka (Day 7 of JR Pass)
• Morning: Kuromon market
• Afternoon: See Others (Day 5)
• Afternoon Night: Train back to Tokyo
Day 9: Tokyo – Ikebukuro
• Lumine, Seibu, Tobu, Animate, Sunshine City, Pokémon Centre, TOKYU Hands, Donqi, Matsumoto Kiyoshi, UNIQLO, NAMJA Town & J-World
Day 10: Tokyo – Shibuya and Shinjuku (can play around with itinerary: Shibuya, Shinjuku, Harajuku)
• Morning: Shinjuku Area – Shinjuku Gyoen, shopping @ Lumine Est., NewoMan, Keio Departmental Store
• Afternoon: Harajuku Area (To do: Visit Kiddy Land (Sanrio), Calbee Plus, cheap accessories at WEGO)
• Evening night: Shibuya (Shopping, Café) – Shibuya 109
Day 11: Tokyo
• Morning: Asakusa Area – Kaminarimon Gate, Sensoji, Nakamise shopping street, Suzukien x Nanaya Level 7 Matcha Ice Cream
• Afternoon: Tokyo Sky Tree (may see Fuji in the distance), Tokyo Salamanchi
• Evening: Ameyoko Shopping Street Ueno (Minatoya Takoyaki, Niki no Kashi Candy Store), Akihabara (Electric Town)
Day 12: Tokyo Malaysia

You've done your research, it's good.
There's a lot in Tokyo that you'll miss due to the stay'/ travel in Osaka-Kyoto.
Tokyo Sky Tree - I won't place my bet on that to view Mt Fuji. Not sure about the observation deck, but all the best.
QUOTE(ZeroWrath @ Dec 11 2017, 10:32 PM)
Hi, I hope it's okay if I ask for some confirmation about transportation - specifically on bus ticket reservation from Shirakawago to Takayama.
Just a bit of context: my trip is going to be Tokyo -> Kanazawa -> Shirakawago -> Takayama -> Tokyo.
So far, I've managed to book bus tickets online to get me from Kanazawa to Shirakawago. The website that I've booked from is
https://japanbusonline.com/.
However, I've been looking for bus tickets that get me from Shirakawago to Takayama, and I can't seem to find this route option for online booking. I was wondering if this option memang is not available for reservation?
From what I've read online, I believe it should also be possible to get bus tickets on the day itself (probably just need to get to the counter early to buy the tickets?), but I would be more comfortable being able to make reservations.
Shirakawa-Go back to Takayama? We took a bus from Shirakawa-Go and it will drop you off at a bus station. From there, we took another bus to Takayama train station. We used the seishun 18 kippu for all the travelling from Nagoya >> Takayama >> Shirakawa Go >> Takayama >> Nagoya.