I had a pretty rough time with jet lag during my trip (still enjoyed it a ton despite this!) but wanted to share my tips to help make your experience better.
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Buy konbini snacks (bread, instant noodles/soup) to bring to your hotel on the first few nights. I woke up around 1-3am hungry the first few nights, and while there are a few 24 hr places I just didn’t want to leave my hotel room at that point. A hot cup of instant noodles would have been a fantastic midnight snack.
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Only in major cities like Tokyo will you be able to find decent food options at odd hours (3-6am), otherwise, many smaller cities and even Kyoto did not have 24 hr places open except for McDonalds, Yoshinoya or konbinis. Even the restaurants that are open at 4am might have a limited menu at that time. We went to Tsukiji market at 4am and was surprised the majority of it was still closed and only like 3 things were open.
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Some train stations vending machines have hot miso soup or corn soup. Surprisingly, not many vending machines at train stations sell snacks and food, they sell primarily drinks. But ekibento places generally start to open around 6-7am.
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It’s pretty helpful to have a hotel that includes breakfast, so you can eat right at 6:30 or 7am. Other restaurant options open at that time are limited (eg fast food, ramen or gyudon).
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Save your fancy meals (omakase, course meals) until the second leg of the trip. My jet lag was pretty bad and I had trouble staying awake for long meals and couldn’t enjoy it as much, and I felt bad for yawning so much right in front of the chefs! Or just try to book the earliest time slot possible, like 5-6pm seating.
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Use your first few days to do things super early. Get on the first train of the day and go somewhere to beat the crowds. Many places are magical during sunrise. We did this for Arashiyama and Miyajima island, and our experience would have been very different had we arrived just 1-2 hours later.
by sirotan88