Note: Feel free to correct me, or suggest revisions! I will edit the main post as needed.

Making reservations on international booking sites to avoid Japanese payment portals:

Foreigners using Japanese sites to make bookings are likely to encounter hurdles like: inputting katakana characters for name pronunciation, having a Japanese phone number, and authenticating credit card payments via 3D Secure.

The first of these issues is trivially solved by using any katakana/kanji converter. The issue of lacking a local phone number is seemingly solved in a myriad of ways including using Google Voice and preparing a physical SIM, but I found there was no practical reason to have voice services when data is available. Finally, Americans may find that portals using 3D Secure will reject all attempts at making credit card payments, and my own attempts at escalating the issue with the service provider or the bank's customer service yielded no alternative avenues.

Ultimately, I searched for equivalent reservations available on international travel sites like Klook or Viator that had none of these particular issues and would recommend such alternatives by default unless you have a friend in the country or a concierge-type service to assist you.

Start in Kyoto

If you are likely to suffer significant jet lag, your newfound ability to wake up early may actually be to your crowd-avoiding benefit. Hit the biggest attractions as soon as they open and enjoy the relative peace and quiet. If this is your first time travelling in Japan, the Kyoto transit system may serve as a gentler introduction to the bus and train system than the relatively highly populated and complex metro hubs of Tokyo. Besides, I found that many shops and attractions in Tokyo are not open until 10 AM, so you might as well ease into it as you adapt to the local time.

Learn some travel phrases in Japanese

In preparation for my trip, I assembled a playlist of YouTube shorts that succinctly covered the most common phrases recommended by locals and travelers. I followed along, repeated the pronunciation, and sometimes quizzed myself to remember the Japanese phrase as I took walks.

Just saying "sumimasen" (Excuse me) and pointing to something can get you by in many circumstances. Many folks in hospitality will understand some English and will relish hearing you speaking their native tongue.

Download Google Maps and Google Translate

These apps are invaluable. Download the maps of places you'll visit and your languages of choice for offline use to save some data. If you save the locations of places you want to visit to a list on the Maps app, travelling between destinations can flow that much more easily. If you save phrases that you search, you can even put together your own travel phrase book!

Get an eSIM

I used Airalo, and offered by reference code to my travelling buddy for a couple USD off. It is possible to get an eSIM in the country using favorable currency rates, but the difference found in shopping for options may not be worth the time or effort.

Follow the steps exactly as described for your given phone brand and model on arrival, though be aware you might want to restart your phone for it to really kick in. For the 10-day journey, I used about 5 GB of data, leaving me 5 GB remaining on my plan (10 GB, for 30 Days for 18 USD). I probably could have been fine with 5 GB over 30 Days for 11.50 USD.

The wireless data service may not be lightning fast, but public wifi is available at almost any establishment. You could opt for pocket wifi for better service, but it is another piece of gear to carry, charge, and mind throughout your journey, and my kit was already full from all the heat-avoiding accoutrement (UV umbrella, sunscreen containers, water bottle, and a hand towel).

Timeline of scheduling

Note that if you are travelling with a group, I would recommend finalizing arrangements at least a month further advance of the following, if reservation windows are open.

4+ months out:

• Book flight tickets as early as you can.

3 months out:

• Book hotels. Consider spending one night at a Ryokan, a traditional inn, if you are travelling as a group. While they are not necessarily budget-friendly, it makes for a particularly immersive way to relax and dine for the evening and prepare for the next day. It is possible to make more spontaneous arrangements in tourism hot spots, but your mileage will vary.

2 months out:

• If you do not want to chance the Ghibli Museum ticket purchasing process on the official site, consider using online booking services that include a ticket as a part of a tour. It will be drastically more expensive in return for your peace of mind.
• Secure teamLab museum tickets. I recommend dressing for photos, and to prepare to wade through knee-high waters for the Planets exhibit. These galleries may take between 90 minutes and 3 hours to take in, so plan accordingly.

1 month out:

• Reserve Ghibli Museum tickets on the 10th of the prior month to your visit as soon as ticket sales are available at 10 AM JST. You are likely to encounter a queue of thousands and deal with server errors due to the incoming traffic. You may be placed in a queue as long as an hour.

• Pokemon Cafe tickets are made available 31 days in advance.

• Check if there are any popup stores related to your interests.

No reservations needed:

• Theme establishments for franchises like Monster Hunter or Final Fantasy were very walk-in friendly.
• Shrines and temples request donations, but don't need advance booking in my experience

Be mindful when visiting temples and shrines

There is much more to temples and shrines than the sights of their architecture and landscaping. Consider reflecting on your own life as you approach historical and sacred sites. How might the prayers of others and blessings offered between generations resonate with your modern life? Enrich your experience by giving thanks for whatever abundance you enjoy, pray that your fortune lasts or improves, and be open to the wisdom that luck changes. It is in examining even your smallest connections to nature and community that you become more self-aware and each location will be dedicated to a different deity, spirit, saint, or historical figure who embodies that unique perspective of life.

I would recommend reading or listening to something philosophical, meditative, or along the lines of self-help to put you in an mindful mindset. When there are so many shrines and temples to visit, trips to Japan thematically overlap with pilgrimages, so make yours meaningful!

Explore

Whatever confluence of culture and economic pressures present in Kyoto and Japan allow for travelers to find their hidden gems simply by letting their interests take them off of the beaten path. Signs can point you down charming alleys that lead to a tucked away izakaya or up to a third-floor library bar, each with their own endearing atmosphere. These discoveries can not only make your trip unique, but help you to avoid congested landmarks. If you find such windows of opportunities, consider not indulging the instinct to comparatively window browse, and taking a spontaneous leap of faith to try something that interests you. Make the most of completely walkable areas!

Odds and ends

• If you want to play a rhythm game at an arcade, consider bringing wired headphones.
• At Don Quixote stores, there are distinct lines for duty-free, medicinal, and conventional checkout, taking the time to know which each checkout area is may save you time and grief.
• Bring a coin pouch and save any particularly small change (1 or 5 Yen) to throw in the offering boxes of shrines and temples. Otherwise, save them for vending machines!
• The Arashiyama district of Kyoto practically closes after 6:00 PM, with many temples closing to new visitors around 4:00 PM.

Things I didn't get that I recommend you look into (or help me understand).

• Shinkansen tickets – I got lost in the sauce of basic fare and super express reserved tickets. I'd get both, try to pass them both simultaneously into the ticket reader, be turned away, ask an attendant for assistance, then be referred to a ticket adjustor. There are probably good guides, but this process was not intuitive for me.
• Metro Day Passes – I could not find a machine that offered day passes, which seem like a great way to save on the many bus and train transfers of travel.
• Pachinko – I got sensory overload as soon as the doors slide open from the blinking lights, and sounds of not-gambling. After feeding cash into a machine, I turned a knob slightly to let the ball bearings feed through, some of which fell into the "jackpot" zone that allowed me to spin a virtual slot machine which might allow me to see a bit of themed media. How does one "zen" out in these circumstances? Maybe it's just not for me.