Just spent 36 days in Japan in a campervan as a couple, thought I'd mention some tips & resources that we would have found very useful prior to our trip.
I see an excellent post here: https://www.reddit.com/r/travel/comments/1w8xz6i/30_days_in_japan_by_campervan/ I would suggest reading this first. I will try to only discuss what has not already been mentioned.
First some context - my wife & I have travelled to Japan before but have not that any experience campervaning before. Went into this a little apprehensive but can gladly say Japan is a wonderfully easy introduction to this form of travel.
Van - nothing but praise for Japan Campers, their vans are discreet (which is important for parking) and team are super responsive. We paid 488,400 JPY for 36 days rental of a Nissan NV350. That prorates to around 2,600 USD a month. Long term rental rates makes a big difference. I unfortunately got into a little accident backing into a railing, the police got involved and a Japan Camper's rep helped us handle all the communication, life-savers.
Parking - https://syachuhaku.fxtec.info/ this is by the far the most important resource I will share in this post. A regularly updated nation-wide map of verified overnight parking spots. As I understand, these are grey-area where there is no explicit mention that overnight parking is not allowed/it is tolerated. Navigate to map section of the website and use the inbuilt translator in your browser. Photo (2)for the crowds you can expect to wake up to at a michi-no-eki/highway parking area. Photo (3) as an example of a spot we found using the website we were the only ones there. If you are travelling in the warmer months (we found September still very warm) the website has a map that filters by altitude of parking spots which can be very helpful as your van probably can't run the air-conditioning without idling the engine.
Temperature - a quick mention if you are travelling in the warmer months, even with all windows open the van runs about 4 degrees hotter than the temperature outside, so we found it hard to sleep if the weather reports had it hotter than 22 degrees at 9pm. We were supplied a fan, but it required our van inverter to be on, which produced a ton of heat, making it very counter-productive. Suggest going to an auto-accessories store to pick up a 12V fan that you an run off your leisure battery, allowing you to keep the inverter off overnight. A final resort is an air conditioned room with a lock at Kaikatsu Club, we spent 4,380 for an 11 hour stay.
Costs - we spent 773,600 JPY across 36 days, which prorates to 4,150 USD per month. This does not include the RV rental fee. We did not cook any meals, but we did not go fancy either. This includes 5 nights in hotels (see visiting cities). This includes 375 USD of tolls & 600 USD of fuel (both prorated to a month).
Tolls & route - looking back, our trip feels like there were two halves. The first half was the whole "no toll roads" on Google Maps approach. This was undeniably great, scenery was gorgeous driving at a gentle pace, pulling over to every mom & pop business that caught our eye. Later in the trip we started getting interested in timing-sensitive events. For example, while in Hiroshima, learnt the drifting championship had a leg being held in Fukushima 12 days later. Figured why not & bought tickets, which set a requirement on distance travelled per day from then on. Using toll roads helped us avoid spending all day on the road while also sight-seeing on the way. I think there is an argument for both ways of travelling.
Trip planning - we had the misfortune of travelling through Japan during one of the rainest periods, but the flexibility afforded by a campervan really helped. As an example, as we approached a hike we were really looking forward to, we noticed rain forecasted for the next few days. We decided to shoot west past it and try our luck again when we would pass it heading back east. Other than using sporting events and hiking trails as itinerary anchors, you could also use performances (personal recommendation for Drum Tao and Blue Impulse shows) and local cultural events. This website is very handy for the latter and is what we used to learn of the Fukuoka summer festival in photo (4)- https://japancheapo.com/events/. Also learned many Shinto shrines stay open 24/7 so we visited both Izumo Taisha and Miyajidake Shrine (photo 5) late into the evening just before parking for the evening.
Visiting cities - we wanted to visit cities like Fukuoka, Nagasaki and Hiroshima but knew driving into the cities to find parking would be a nightmare. Use your favorite LLM to query an appropriate transit hub close to, but not in the city center. This way there will be ample, easy to access, reasonably priced parking. Then book yourself a modest hotel a short train ride away in the city. Who knew a private poo could feel so good after a few weeks in the van.
Tattoos - I am unfortunately tattooed like OP on the other post. Anytime Fitness (didn't think of this) and Kaikatsu Club (our bread and butter) are great suggestions. I would also add using the search terms "tattoo friendly sento" and "family/private bath" on Google Maps. 2,500 JPY for the family bath in photo 5, a slight premium but you will be able to visit far more onsen's this way.
Food - Costco for fresh fruit, hit up supermarkets at 8/9pm for discounted sushi & bento's (look for the microwave before bringing back to the van).
We hope that was helpful, feel free to post any questions and we will try our best!