A few observations...
First, as you are probably aware, going to Japan in mid-22 is still quite iffy. The virus is still going around, so keep doing research, but I wouldn't start packing those bags just yet. Also, you don't state where you are flying from, and how many time zones you are crossing to get to Japan, but it looks like you are landing at NRT in the early morning, and have a full day planned - unless you can sleep well on the plane, you might very well arrive as a brain-dead zombie, and that is no fun way to see Tokyo. You might consider catching a few hours of sleep somewhere. I suggest you try to keep a light first day. And to be honest, I don't understand your plans here - you clearly state you have no interest in anime and manga, but then you write you want to go to Nakano Broadway, which is Anime and Manga Central.
By the way, you say you're interested in museums - unless you have a big interest in camera history, there might be a lot better ones for you. You might browse this listing of over 900 of them:
https://www.tripadvisor.com/Attractions-g298184-Activities-c49-Tokyo_T...For your 3rd day, you asked for other ideas for sights. It's unclear if you've been to Japan before, but I highly recommend visiting a couple of Tokyo's traditional gardens - they are gorgeous, uncrowded, inexpensive, and give you a good immersion in real Japanese culture, if that is what you're interested in. A few of the best are Kosihikawa Korakuen, Rikugien, and Kiyosumi.
https://goo.gl/tAECfMYou also might visit some great places for city views. There are some excellent and popular ones of course like the Skytree, Mori Bldg, and Shibuya Sky. But if you want lesser known gems, there are others like the I-Link Tower (45 floors up, near Ichikawa Stn). The TMG is nice too and free, though trumpeted in every guidebook and flowing with international tourists. Another option if you have an afternoon is go see Kawasaki or Yokohama - they have a different environment, and both with some good sights like the Minka-en (plus, ig going in June, the Hydrangea Mountain is really nice) and Kawasaki Daishi, or for Yokohama, Minato-Mirai, Chinatown, and the beautiful Sankeien Garden.
For Onomichi, I don't know what your ideas of a "beach" are, but you might find a lot less than you expect, unless you mean going out on to some of the islands.
As mentioned above, I wouldn't get the 14-day pass. Just get regular fare tickets for Tokyo-Osaka. You might however get the Kansai-Hiroshima Pass. This has the added bonus of being able to take the 'faster' Nozomi trains, at least for the Tokaido portion. However, your Day 7 plan is confusing. You previously mention staying on Hakata Island, then you suggest taking the bullet train to Hakata (Fukuoka City)? If the latter, I lived there many years and know the place quite well. There are some good sights, but in your position I'd choose seeing Hiroshima or Himeji.
Your Day 9 plan makes no sense to me. You first state you want to go in mid-'22. then you say you want to see the autumn leaves - that is typically the 2nd half of November.
If you want to get to/from NRT at Ueno, then the Keisei Skyliner might suit you quite nicely. Be aware though that if you are arriving on a weekday morning, the trains and subways can be horrifically jammed.
Lastly, if going with your SO, instead of the Air B&B, why not spend a night or two in a Love Hotel?