The cost of getting around once a person gets to Japan is one of the most under-recognized aspects of traveling there. People budget thousands of dollars (or the equivalent in other currencies) for airfare, hotels, lodging, meals, shopping, and venue admissions, and then freak out when they discover that they may have to spend several hundred dollars to get from place to place, even though they have an itinerary that involves considerable long-distance travel. For some reason it doesn't occur to people that high-speed trains are not particularly cheap, or that the transportation network isn't a seamless operation run by a single company. Rail passes can be provide amazing cost-savings if you use them to maximum advantage, but they are not always the best solution.
You need to look at the available passes, do cost calculations, be willing to tweak your itinerary to get particular value out of a given pass, accept that no matter what pass (or combination of passes) you get there will still be some out-of-pocket costs for individual tickets or IC cards, and recognize that rail passes have some advantages and disadvantages that go beyond a strict cost-saving basis. And unfortunately, you need to be willing to spend a LOT of time figuring it all out. There are no simple answers. People on these forums love to proclaim how "easy" it is to travel on Japan on a do-it-yourself basis. Ha!
Here is the Japan Guide page on rail passes:
https://www.japan-guide.com/e/e2357.htmlYou have to go into many of the sub-pages to find the information on passes that might work for you, and you need to carefully study the information on how to get to and around the places you are going to. Recognize that some means of transportation can be much faster than others, and that in many places the trains and/or buses do not run very frequently. Learn how to look up schedules on Hyperdia and other sources as needed. Figure these things out before you make any final rail pass decisions...
In my experience, the best way to plan a trip to Japan that makes good use of rail passes is to integrate transportation into your decision making from the beginning, rather than coming up with a fixed list of destinations and dates and then try to find a rail pass that works for it. Why so many people advise you to figure out your entire itinerary first and then find a rail pass to match is beyond me. Ideally it is an iterative process, I believe.
If you have more money than time, the simplest solution is to go ahead and get a nationwide JR pass. (It will also get you to Nikko and part of the way to "Mt. Fuji" if you choose routes that involve JR, and there are some benefits beyond cost savings.) But if you want to find the absolute least-cost solution, then you need to do more research.
So this post isn't really going to help you much, but the point is simply that you need to spend more time figuring this out. There doesn't appear to be an obvious easy solution in your case. Just take a few deep breaths, don't panic, and do be patient. You have time before cherry blossom season (although don't wait TOO long to book hotels for that time frame), so don't let all this become a nightmare. You can keep coming back to the forum for advice on specific questions, but in the end you are basically on your own to figure out what works best for you.