I would like to stay at $100 range (better under like 75 range since I do have to pay for total of 16 nights and the first 2 nights is already pricey for my standardscjust did it for convenience). Also prefer near main stations and safe clean hotel.
For the former, it is each to get hotels of less than $75 USD (i take it as USD? Am i right?) In Japan there are business hotels which are about 50-70 USD per person night. The lodging is simple though you may have to sleep diagonally if you are not Asian. For the latter, I have not found any accommodation in Japan that is neither clean nor safe. A hotel would surely be less inclined to be so.
What could be a problem is that your dates are mid to late April which may coincide with the cherry blossom blooming period. Peak travel season in Japan. The cheaper accommodations are disappearing as you are reading this. Popular cities may be booked out, and sometimes you would have to stay in the towns and smaller cities outside the city. (This being Japan, this means a 30 minute or less train ride away. Usually such accommodations would also be cheaper than being in the popular city.)
Day 2 Many walks in Shinjuku. If you are staying in a place with a gym, you can exercise till you drop. Helps with the jetlag. About half an hour to 1.5 hours from plane to train station. Another hour for train. Hour to Hour and a half if you are getting a train pass from the ticket office.
Day 4 The JR Ticket Office is far more crowded at the airport. Changing your pass in Tokyo would probably take less than an hour. Do make all train seat reservations at this moment to prevent wasting time queuing again in the future. Kanazawa has only one hotel with an onsen (the rest are hotels with hot baths meaning just hot tap water). It is not a ryokan but it does have tatami floored rooms from memory. That said, this also means it is (the most) expensive. Kaga onsen is not too far away, but if coming from Tokyo I guess you would not want to travel any further. So in summary, find a cheaper accommodation, there are probably other chances for ryokans and onsens at other points during your trip. I don't see the need to change the Kanazawa day. I would spend more time here though. The travel from Tokyo and just checking in to the hotel would take a majority of your time.
Day 6 and Day 7 No idea why you would spend 2 days in Takayama. Would rather spend a day in Takayama and 2 in Kanazawa. The usual practice is the morning in Takayama (morn market) and to spend an evening or overnight in Shirakawa-go if farm houses (it has an onsen from memory) are your thing. Someone else might mention why Takayama is worth two days. Think he said hiking the mountain lands of Takayama. Plus the mountains away from Takayama city centre has onsen ryokans.
Foodwise: Takayama has good soba. Kanazawa has good any type of food. I particularly liked the noto peninsular wagyu beef at this korean BBQ place (Japan, 920-0852 Ishikawa Prefecture, Kanazawa, Konohanamachi, 9-13). Had a pal who tried and loved a place called Golden Curry.
Day 8 You have to leave early and expect to return late for this. Check the last shinkansen to Kyoto from Hiroshima. Also note Miyajima night fall time (Itsukushima shrine is to be seen in the day/ night + low / high tide).
Kyoto in general: I recommend 3 days minimum for first timers. Five, if you ain't a fast pace traveler (I presume you are based on the number of days spent at each location so far). One for North (Kinkakuji, Ryoan-ji, Ninnanji, Myoshinji, Toei Studio Park) One for East (Higashiyama districts, Nanzenji to Ginkakuji via Philosopher's path stopping by Eikando and Honen-in, and Heian Shrine, with dinner at Gion/Potoncho) One for South and Arashiyama (Only thing south is Fushimi Inari, Arashiyama is self explanatory). You can see Kyoto station mall and teramachi-dori during dinner. Central Kyoto, Kurama/Kibune, Enryakuji, Sanzen-in is for people with more time. Uji and Nara outside Kyoto and not what I would consider under Kyoto days. Note that Fushimi Inari is 24/7 so early morning in the the dead of night is still accessible. Are you fine with hostel living? If so, I have a few I can throw your way.
Osaka in general: Day time sights like the castle, USJ, and cup noodle museum is a real ?. This depends on your interest. If it is still cherry blossom season, the mint museum is the place to be. Usual practice is to day time in Kyoto, and night out in Osaka. For 2 reasons: Kyoto attractions close early Osaka has much more night life
Day 13 Note that you should get the Hakone Pass for Hakone. Hakone has some charming ryokans but they are considered over priced. Since you aren't going to many other onsen towns, perhaps you don't mind footing the bill? If not, head to onsen town like Kusatsu.
Final Day Probably taking the train to the airport? If so, traffic won't be so far. Trains don't stop for red lights.
Doing Kanazawa/Takayama later has two benefits: 1. It is a mountainous region and would be slightly warmer if you do it later. 2. Higher chance of seeing cherry blossoms in Osaka and Kyoto Major bad point, is that hotels would be much more expensive. (note on popular cities mentioned above)
For individual sites on Showa day check this website for opening and closing times and for closed days. some attractions give free entry on public holidays. Kenrokuen!!
APA are great! Better but slightly more pricey than Toyoko Inn IMO. There is also the Hotel Nikko chain of hotels. So many business hotels in Japan... As mentioned, they are all safe and clean (I've stayed in a 20USD about boarding house before, and though it looks run down it was still clean and safe).
On your train questions, I answered above.
Cannot help on Takyubin. Never had to use them. Whether I am traveling solo or with others, I use one backpack and one only. Did two weeks in winter and two and half weeks in autumn with always one backpack. The key is to pack one jeans for each week, sleep in shorts that can be used on not so cool days and presentable enough to walk about the hotel, and to find a laundry machine.
On clothing, normal jeans and shirt. Layer extra socks if you feet feel cold. (Wear the outer pair of socks the next day to save on over-packing) Wearing a jacket or a thermal underwear helps greatly. If it is not enough just use an extra shirt. (Again re-wear the outer shirt the next day, or you could use it only as an outer shirt and tell your friends when you show them your photos that it is a "jacket"). If you are adverse to cold, mufflers or a beanie helps. I don't see the need for gloves or scarfs.
In Japan, the best way to beat the cold is hot springs. Just go for a dip (10-15 minutes) before breakfast and you are set for the day. I did -8 degrees C in just a Polo-T and jeans.
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