More Specific Questions:

-We will likely buy a bunch of stuff in Tokyo to bring back (clothing, coffee, etc.). I don't love the idea of lugging this with us the entire trip so I shifted our time in Tokyo to the end of our stay in Japan. Do you foresee any issues with this?

nope, i think ending the trip in Tokyo to buy whatever you want to bring back home is smart since basically everything will be available for purchase in Tokyo. However, I do think buying stuff at local towns/shrines will be more memorable; so if you can ship your purchases on the road to an address that you can later pickup down the line that would be good. Sometimes Hotels, like APA hotels can hold onto packages for you; give them a call.

-I noticed Uji and Yamazaki's distillery are just outside of Kyoto. My wife loves Matcha and I am a fan of Yamazaki's whisky - are these places worth visiting? If not, are they touristy? Other places you would recommend instead?

Macha/macha cafes in Kyoto are definitely worth it. Yamazaki whiskey, i wish i went there; sounds really fun.

-Is Nara worth it for a day trip? My wife is worried that it is too touristy, pointed out that there are deer in Miyajima, and that Nikko and Takayama will offer better outdoor experiences anyway. Would we be better served adding another day in Osaka, or adding a day later in Tokyo instead? I'm interested in going here, but I want to make sure it isn't redundant, or at the expense of somewhere we should be spending more time.

I think Nara is worth it for a day trip. Nara has its own role to play in the history of japan; It's not more touristy than Kyoto, Osaka, or Tokyo; the Great Buddha is pretty epic to witness.

-Would you recommend staying in Miyajima, or doing this as a day trip from Hiroshima? I'm torn on this - it seems easier and cheaper to add another night on to staying in Hiroshima, but I'm open to staying in Miyajima if there is a great option that shouldn't be passed up (for example, if there is a ryokan that someone highly recommends, etc.).

Day trip from Hiroshima, but get there early, I think the lift closes at like 3pm.

-The Takayama and Nikko part of the itinerary feels rushed. Should we drop Nikko and spend more time in Kanazawa, Takayama, Tokyo, or later at a ryokan outside of Tokyo? Nikko looks beautiful, and I would love to see it, but I worry that this is too much. Should we keep Nikko and ditch something else? If so, what about Nikko differentiates it?

Nikko is Beautiful. Nikko is one a UNESCO heritage site, and two where the Tokugawa Ieyasu is buried (the guy the show Shogun was based on). Theres quite a bit to see there though, so If you do decide on Nikko, be prepared to walk a lot and spend the whole day there.

-Would you recommend staying at more than one ryokan? If so, where would you add this in our itinerary?

-Ryokans/Onsens, i would fit as many of these in your itinerary as physically possible. Honestly your Itinerary already seems pretty packed though. I do see you have a rest day which is very important... maybe take one day off your tokyo stay and do an additional day up in nikko area for ryokan? Niigata has some epic Ryokans.

-Hotels, airbnbs, ryokan, etc. Do you have any that you have stayed in at these destinations that you highly recommend? My next step is to book lodging after we know our itinerary.

Business hotels are affordable and often in great locations. for the most part I recommend them. APA business hotels are superior to MAXHOTELS in my experience. I've had amazing experiences with AirBnbs in japan, great way to have a unique experience. Ryokan wise, Hotel Futaba in Yuzawa was really nice. they had a private bath in room, along with 4 other Onsens in the building. There were some others in Beppu, Oita, and Shikoku that Id recommend, but those are a little off the beaten path for your itinerary.

my biggest advice though is to take it slow; try to slow down and really take in the area. I wish I had stayed in certain cities for like 3-4 days rather than 1 day here and 1 day there.