For me, I find that 2 months will give you a good taste of the main island of Honshu which is actually much bigger than most people think it is.
One thing to consider is how much you are willing to spend per day, how you will get around and how you will book your accommodation. If your budget is too tight - then a lot of the suggestions we might make will be out of your price range.
I've traveled Japan more than most and have a few posts on my main page. You should find a post for most places on JG and even a few new ones.https://www.japan-guide.com/community/mfedley/
When it comes to accommodation, booking in advance can be helpful and looking at conditions can be helpful. For example - I tend to remember that Toyoko Inn's allowed you to cancel up to 4PM of the day of checkin and they are normally well priced near train stations. If you want to travel comfortably but not too expensive - then business hotels can be a godsend. I rarely stay in traditional accommodation anymore as I've been there done that. It's worth trying for a few nights to see if it's something that you like (sleeping on futons). My main problem is not sleeping on futons - but my fussiness in thin mattresses which might happen at my price range hotels.
To give you an idea of how much I spend - my winter vacation (23 nights) is costing me a little under 140,000 yen which includes a smattering of onsen hotels, a whole house on Yakushima for 4 nights, some kaseki dinners and the like. I often book through:
is also good for Tsurunoyo Onsen in Nyuto
If you are in Japan for a long time - then using the Japan Pass will probably not be worth it for you. In locations such as Kansai, having a base city can work out really well as there is lots to see within day trip territory. Hiring a small apartment for 2 weeks in Kyoto or Osaka near a train station could work out reasonably economical.
There are also some good bus passes and the 18 Free Kippu which could be helpful for slow but long train travel. Another thing to ask is are you willing to drive a car? In general, I will never drive in major cities like Osaka, Tokyo or Kyoto but will hire a car in rural areas. Another slow but lovely way to travel is to catch the train north to south on the west coast of Japan. You'll be in some of the most beautiful places in Japan and prices and tourist numbers will be low due to slow travel times.
That would allow you to hit Osorenzan (Shimokita Hanto). Hirosaki, Sakata, Dewa Sanzan, Sado Island, Noto Hanto, Kanazawa, Kinosaki along with two of my favourite areas in Japan (Matsue + Hagi).
Another option is to spend 2 weeks in each general area (2 weeks Tohoku, 2 weeks Kanto/Chubu, 2 weeks Kansai, 2 weeks Chugoku. If you want to get away from the crowds and have more flexibility, then I would highly suggest both Tohoku and Chukoku as great areas.
I've already rambled enough....