According to Google, Kurama-dera opens at 9am? Kiyomizudera Temple opens at 6am.

Looking at Ubuya hotel in Kawaguchi-ko but no availability for the next 12 months. I was thinking it'll be easier taking a day trip from Tokyo to Mt Fuji?

I'll put Miyajima on my list for my next visit.

What time do you arrive in Tokyo on Day 0?

Here’s another example from day 3

11:00am: Walk north through Kitanomaru-koen Park and then visit Yasukuni-jinja Shrine. Do not miss the controversial and interesting Yushukan Museum at the shrine
12:00: Take the Shinjuku Line subway west to Shinjuku. Eat lunch somewhere in Shinjuku

“Do not miss the controversial and interesting Yushukan Museum at the shrine”

The Yūshūkan Museum is one of the best in Tokyo for English translations of the exhibits. Also, you won’t really see much of anything that will strike you as controversial unless you put aside time to read the eyebrow raising alternative version of history presented there.
If you are genuinely interested in finding out why it is controversial it will take a full hour at the very least (unless you have a knack for genuine speed reading) to go through the rooms and take in the displays and their descriptions. Merely popping in and going out again in accordance with your itinerary would be a waste of time unless the aim for the visit is to tick it off a list.

My bad, I mixed up Kurama-dera and Kifune-jinja (the latter is the one that opens at 6AM.)

Look into volunteer guides. There are organizations in Tokyo, Kyoto,... that will aet you up with a guide (you pay her/his transportation and lunch) which makes sightseeing much easier and you make a person to person connection.

I don't really like those as I would find it very awkward and boring with just the guide and myself. I would prefer a small group led tour but I cannot find very many.

Your itinerary is full of a lot of great stuff. The only thing it's missing is spontaneity.

I think it's safe to assume that the OP will fit that into the gap between "9:20am Purchase bus pass and Shrime tickets at Tourist information Centre" and "9:30am Take 2B bus to Stop 7" on Day .

Overall impression - the itinerary is way too specific. You might have days where the weather is one thing or another, or your feet are beat after walking around all day, or whatever else. So my general recommendation is to just have a list of potential things to do in each area, and every day you're there pick a thing for the morning, a thing for the evening, and fill the in-between as you go. Obviously this excludes anything where you need tickets in advance.

A few specific observations:

Yushukan at Yasukuni: if I remember right, a lot of the exhibits are primarily written in Japanese; you won't always find English 1:1 with it. "Controversial" - it's not that wild and crazy. Just that some parts of how they describe the lead-up to the war and post-war effects through Asia are... well, an interesting perspective 🙄. IMO I'd put this low on the list. I saved it for my 2nd trip over.

Senso-ji: For major tourist attractions like this, I'd plan on getting there early. It gets really busy. Zojo-ji is an alternate option; when I went there it was far less crowded. It's also right by Tokyo Tower.

Fushimi inari: This is actually a really large and expansive area; you can spend quite a bit of time meandering around. It's one where I think it's good to plan to spend extra time and just "be there." At Fushimi, and Arashiyama, and other places... so many people are just glued to their phones taking selfies and totally miss the actual experience.

Nara: You have two day trips to Nara? I'd consider doing just one, and maybe have a day trip to Himeji as well. Himeji castle is really pretty impressive.

How is your "restaurant ideas" area blank?? That's like the first thing I work on when traveling 😂 On that front, starting in Tokyo...

There are quite a few little restaurants in Tokyo Station. Look up "kitchen street." Worth checking that out. I'm a fan of Tonkatsu Suzuki.

If you end up in Asakusa, there's a little fried chicken spot called "Yukari." It's just like a window and you grab and go. Really good, and cheap.

It's worth getting to an izakaya and having that experience. Tatemichiya is somewhere around Ebisu station, and it is a whole vibe.

In Kyoto there's a good hole-in-the-wall yakitori joint, Daikichi, just east of Sanjou station on the Keihan line.

A bit south of there, probably closer to Gion-Shijou station, is a good gyoza spot - Hohei.

Further south yet, off Shichijou station, is a really inexpensive spot for ramen and fried chicken - Ramen no Bonbo.

If I remember right there are several ramen spots in Kyoto station itself, like a little section dedicated to them. Ichiran might be worth the experience (they're sprinkled all over) and they're open late or 24 hours.

In general for restaurants... it can be good to have alternate plans, or just wander around. A lot of places are tiny and fill up fast or might only have a few spots for walk-ins.

Sushi is its own discussion and a wide spectrum of experiences.

Other recommendations:

Get a Suica/Pasmo/whatever, they are super practical. BRING GOOD SHOES.

I echo this sentiment. I just got back from three months in Australia, Singapore, KL, and Georgia. Last year, had two three-four week trips. In all cases, the pleasure of the trip was structured days offset against days just walking around the neighborhoods, dropping and adding things on the fly. I typically planned maybe one or two big things per day on busy days; the remainder of the day was spent just wandering predicated on how I was feeling. I deliberately put in one or two "zero" days per month, just to nap, watch TV, etc. Three weeks is long enough to want those zero days. The older I get, the more I really value "less is more" when it comes to enjoying travel, but, of course, all of this is really an experiment of one (in this case: you).

Thanks for the advice.

I've marked the places which have pre-booked tickets in red.

I think I might scrap my daytrip to Nikko and have a free day in Tokyo. I'll also scrap my 2nd trip to nara and have either a free day or a trip to Himeji Castle. And have Hiroshima and Mt Fuji free days if needed, i can always go back there next time.

I think people need to avoid a tick off the box mentality for Japan. I think it sets people up for disappointment. I'd never in a 1000 years visit the bamboo groves in arashiyama but yet it's on many people's list and its magic is only in the eyes of contrived photos

I think the magic of the Arashiyama bamboo grove and Fushimi Inari shrine is if you experience it in quiet secluded situation being alone. If the place is packed with tourists like Shibuya scramble crossing then the magic is gone.

Deleted

Dependent on the time of day you arrive in Tokyo and what time you can check in to your hotel room on day 0, you may have some time kicking your heels and be looking for something to do after dropping your luggage at the hotel.