Well, it's been a while since I've been, and I've never travelled out of the cities much, was always there with various University groups or workshops.
But.
I did slip out once with family and I think the thing I remember most was going to the owl cafe.
That was an experience I don't think you can get anywhere else in the world.

The only time we didn't use the pre-arrangements for where to stay, I went through AirBnB. Which worked great and was very reasonable in pricing. Also the hosts were willing to help answer questions.

Something I recommend sorting out before you go: your phone situation.
A lot of plans turn out to be far more expensive than you would expect when you are travelling; please look into either getting new phones and a phone plan while you are there, since you will be there for a while, or looking at a program like the GoogleFi one, where travelling will not cause an increase in your rates for the duration.

Most of the international airports in Japan (I can't say all of them for sure, lol, haven't been to them all) will have an information/help booth that you can pick up good information from, it's an excellent supplement to your research; they should be informed about things like recent construction which might not show up when you are looking at making your original plans. The airports will also have shops selling SIM cards and phones if you are going that route.

Then, the last piece of advice I have, is to find something small and reasonably priced but iconic to your own home region, and bring a BUNCH of whatever it is, that you can give out as gifts during your trip.
You'll find that people really appreciate it, and it will open doors as they will be more friendly and willing to go out of their way to help you.
I'm not talking about anything big.
But for instance if your area is known for lavender, then bring lavender wands and write up a small explanatory card for them. Or if your area is known for its pecans, prepare some small gift bags of the nuts in nice ribbons, with the name of your region. That kind of small tourist-y souvenir-like thing.
You can gift them out as you go, to people like your landlord/airbnb host or the hotel concierge, and to contacts you meet, potential friends or business partners, etc.
Because most of the best places to go, the best things to do, the most interesting finds and events, all of these won't be easily found if you don't have contacts.
And this is way to quickly get contacts.

Oh.

And try the street-food. It's great.

Congrats Fire on you trip to Japan!

I still haven't been in Japan, so I don't know much, but I still think these few things I know might be helpful

If you're going to Japan early April, I think there may still be sakura blooming in the northern Japan. By typing 'sakura forecast 2024' you should be able to see a forecast with a map that shows when sakura starts blooming (looking at blooming sakura is called 'hanami' 花見, Japanese love to do it every year, hence the blooming forecast). The photos each year look absolutely stunning, so it would be sad to miss, especially since you're in the right time for that. I've also heard that sakura blooms only for few days, so if you decide to see it, the timing is of the essence (though I'm not sure how true is that, I haven't been there).

Another seasonal occurrence is the rainy season, 'tsuyu' 梅雨. I've read it starts early June, there may be some variations every year, I'm sure there is a forecast for it too. When it starts, it will heavily rain all day, all night, all day and so on. Your trip might end before the rainy season starts, then there will be no problem. If it starts earlier while you're still in Japan, I think it will be best to plan some indoor attractions for these last few days

About food, my japanese teachers said that it is a common occurrence to have an upset stomach for first few days after coming to Japan due to difference in bacterial flora - it might be a good idea to take some medicine for that.
I also think Osaka is famous for its takoyaki たこ焼き, but it might be a common knowledge

I'm not able to answer if shopping for men's clothes is ok culturally. I think their first thought might be that you do not know that these clothes are for men, and the second that you might be an otaku? I don't know how ok it will be, though I doubt they will say anything to you anyway. But I think there may also be another problem. Asians have a very, very slim build. Depending on your genetics, on your build and on clothes style, these clothes may be too slim. Especially men's clothes - I have 180 cm and as a woman I am not able to buy any men's clothes in Poland where I live, because my hips are too thick.
My japanese teachers didn't say anything about buying clothes, but they warned me about buying shoes - the biggest shoe size for women in Japan is 'L' and it is equal in shoe length to european size 39, but these shoes are so narrow they don't fit at all. And buying it anyway means wounds on your feet - yes, they did buy it...

Similarly, hair dressers or japanese hair dyes might be a bad idea, though that also depends on your genetics - Japanese have a very thick and straight hair, so their dyes are very strong and destructive for less thick hair, they are also cut and did very differently. My japanese teachers always said to ask a hairdresser in Japan if they did non-Japanese hair beforehand because of that.

When you're in any bigger city, like Tokyo, I know there are hidden gems there. Very well hidden, in a very narrow streets, so narrow one person barely fits there Look for Hanabusa Inari Shrine in Tokyo on youtube for example - I've heard there are many shinto crams like that, in various cities. Because these cities expanded while there were already some shinto shrines, so they were 'absorbed' by the very tall buildings around them. I think it might be magical to visit at least this one shrine And it might be worth it to sometimes go into narrow streets like that.

Ohhh!

And, if you have any tattoos, get something to cover them up with, and practice the covering makeup techniques if your tattoos require it.

There are a number of places that won't let you in if you have tattoos, and the culture around tattoos there is very different.

Just general things before I dive into the touristy stuff in another message because it's gonna be too long otherwise.

For booking websites there's also Rakuten Travel and Yahoo in Japan but Booking/Agoda are generally the less expensive ones.
Also you've chosen the very big tourist season so you might want to book fast because it's only going to be more expensive as time as on.

I'm not eligible to the JR Pass so I can't tell you anything about that, except to use Google to calculate. I know it got more expensive but with such a huge trip it might be worth it.
Also JR has a thing called the JR East Tohoku pass which is a lot less expensive but also more limited.
Otherwise you have the choice of not using the Shinkansen and going slower on normal lines. Either way you're looking at an insane transport budget.

As for your question about clothes it's going to depend on the store, Uniqlo is going to be fine, a very small boutique might be more difficult. Also, there's H&M and Zara in Japan too. And there have been years when I have been fine in shorts at the beginning of April, not in Hokkaido though.

As for tattoos, it's getting better but the general rule is everyplace that's expensive or very family friendly is going to be annoying about tattoos. But seriously, I do have one and no one ever told me anything except at one hotel.

Food and travel informations will be coming when I have more time to dive into my memories.

Holy crap you are finally getting your Japan trip!! I'm so happy for you! Take plenty of pictures and send the group chat updates!.