Here's two relevant points to know about Japan:

1. They love making ranked lists and checklists. Seriously, they have stamp rallies. This also means those with limited time might want to see if their interests align with a random tourist list (or even those from tourism agencies and guide companies). If it exists, it is on some list.
2. Tourism is very well developed. Tokyo, Kyoto, and Osaka all have a lot to do depending on your tastes. Many English checklists for the "Golden Triangle" won't be 100% accomplishable even if you had over 2 weeks. Japanese salary workers don't get that many days off per year so they tend to stick to 2-4 day itineraries of fast paced checklists.

It isn't just the journey time some day itineraries don't account for, it is pacing over multiple days in addition to not accounting for weather.

Here's my advice as someone who has taken her share of pajama whistlestop bus tours, has designed & carried out a few group day trips in destination locales, and also travels solo to Japan (repeatedly)

How to plan a checklist trip with less heartache and muscle pain:

1. Be pragmatic and also at times, ruthless. If you go on a group pajama tour (nicknamed such as you basically have so little time to make it through the tourist checklist, you might as well not change) then the packed itinerary is set for you at the cost of choice and sleep. If you set your own itinerary, be honest about what you want to see. There's plenty to see in Japan and skipping something on someone else's checklist doesn't mean you necessarily "missed out"*. Don't know what you want to see**?
2. Set your priorities. Go through the interests/itinerary and label them P1-P4, P1 being the highest. On the fence about skipping something? Throw it into P3, go look at a few photos later, and see if you want to upgrade the priority.
3. Move lower priority items off the "schedule", noting their general area. This gives you the some room in your schedule to hit the fixed timings and higher priority sights. Add nearby low priority items back while you're already there if time allows. As LapLap mentioned, some of the transit schedules can't be worked around your current fixed timings for tours and reservations. The food tours at slightly earlier than dinner times require the rest of the day to be more flexible. If your schedule is too full, you will be late for fixed timings. Japanese culture is generally very punctual. Late = They'll keep your money and you won't get to go on the tour.
4. Schedule your down time AND be-present-time to wander if you really follow schedules. Maybe you have your checklist and socials to post (FOMO), but even pajama tours know to schedule "free time" or guests will end up sick and too tired. Plus out of clean clothes and unkempt/athleisure isn't the every day style in these cities. Some people physically can't handle 4 days of 15-20+k steps in the heat. Others feel really socially isolated and would greatly benefit from a video chat home or "comfort tv show" or food. I'd suggest at least 3 hours every 2.5-3 days at the pace you have planned. You know your physical limits better than people on the internet. Some people like the whirlwind to the point of needing a vacation to recover after vacation like Agneisse but knowing your limits and interests is important to avoid actual disappointment. Not having any be-present time to wander would definitely be missing out, IMO. That's my own learned experience. There's FOMO due to peer pressure but actual regret from missing experience memories as that's what my (not-great) memory and feelings retain the longest.
5. Review your next day or two itinerary at the end of a day. Be ok with adjusting things based on what you did like. Do more of that. Defeated feeling due to planning failures multiple days in a row? Book that day trip tour and follow the guide (shift the responsibility, I won't tell) or just do 1 P1 thing and treat yourself to something happy. We're not the ones spending your money, enjoying your vacation

* Things I have not done which are on various peoples 1st time visitor must checklists - a lot, actually. Tokyo Tuna markets, climb to top of Mt. Fuji, just about everything Ghibli, Pokemon, and Disney. I have been to probably 60% of Japan's prefectures? Do I regret trading them for sleep, travel outside the big cities, or onsen time? Not really. Perhaps will accompany friends and their families to these places on a future visit.

**Don't know what you want to see - easy mode is to look at paid group tour itineraries with some pictures and try to duplicate it if your interests align, allowing some variance for non-guided public transit vs their chartered vehicles or guided local transit. These are actual attraction checklists which people have generally paid to see and their peers also accept as "must see destinations", though personal experience says to check for "shopping time" and odd "why is this an attraction" which may be bio break bathroom stops.

Look for a few other tourism related videos from YouTubers you don't normally watch Japan YouTuber thread I enjoy some of the channels but logically know I won't be replicating all of their trips (Solo Travel San is a car ferry otaku and Suit Train can sit longer than I can, which is impressive)

Klook Day trips is a booking portal with local operators Klook - Has Anyone Used Recently? which specializes in Asia. Asians do checklist travel well (see limited time off again and checklist travel is also cultural)

Sample Kyoto & Nara - https://www.klook.com/en-US/activity...ay-tour-kyoto/ We see this is an 11 hour trip. If we look at the afternoon portion of the schedule
Sample Tokyo Highlights https://www.klook.com/en-US/activity...kId=07887b9bfd