2 weeks solo in Japan – travel advice/tips needed

I'm traveling to Japan 07/31 – 08/14.

I have no itinerary set and could use some advice.

It's been a dream to visit Japan and here are the vibes that I'm chasing:

• high end thrift stores
• great food
• traditional ryokan experience (preferably on the countryside, mountains, or near the ocean)
• tattoo friendly onsen experience. I could also cover up my tattoo with a dry fit shirt if that is also acceptable
• I'd like to go scuba diving. I was set on Okinawa but I realize that might be a bit too much for this trip so I'm open to other locations.

I want to spend time in Tokyo of course, but what about other places? I'm kind of a slow traveler and I like quaint moments.

I'd greatly appreciate any itinerary ideas and accommodations recommendations.

Edit: I'm also a huge Kill Bill and Studio Ghibili fan – so visiting places that were included in the film or inspired Studio Ghibili animations would be ++++.