Booking places for two months of travel?

I am spending two months (May 20 - July 20) in Japan - what are some of the best locations to stay for a few days at a time?

I am limited by language ability so need to largely travel by train/bus. I would like to visit the wides range of islands and locations - many of the "destinations" from japan-guide.com !

I have started to research Temple Lodgings and Minshuku to stay at during my travels.... but I am feeling a bit overwhelmed.. are there any great resources you recommend that I look into?

Thank you and sorry for the long post

Have a look at this website. There are many locations and destinations to choose from.

Some people like to roam and change hotels every 3 days. Some like to stay at a hotel for 5-7 days and make one central location their home base. Tokyo, Kyoto, Hiroshima, Fukuoka, Sapporo etc.

I'd suggest looking at all the destinations and finding the ones 'you' wanna see, then look for a central location you can work from.

For Japanese accommodations you can use Japanican. Google it. This third party website contacts the lodging directly and may take some time, however it is good if you are not comfortable navigating Japanese hotel booking websites (Agoda, Booking.com, etc are not comprehensive in Japan).

From May to July you have effectively about 61 days.
If I were you I would split it to 6 regions and using 10 days for each region. The 1 day is for transiting to and fro the airport.
The six regions would be:

1. Kansai- This is where Osaka, Kyoto and other fun places are. From either of these cities you could make a daytrip to various onsens (Kinosaki, Arima, etc) or even overnight in one of them. Other day trip options are Nara, Kobe, Himeji, Ise, the list goes on. Also staying overnight in Mt Koya is a unique Japanese experience.

2. Chugoku- This is where Hiroshima is, a solemn city that was a-bombed; Okayama, having a beautiful Japanese landscape garden; plus the many small towns along the northern coast. It is also one of the gateways into Shikoku.

3. Kanto- This is where Tokyo is. Need I say more? A multitude of daytrips are possible from Tokyo. Ask anyone on the forum for help here if you need some.

4. Chubu- Where the world famous Mt Fuji is. Also Kanazawa, a castle town with a beautiful garden. In between these two are the Japan Alps, a large stretch of mountains that promise scenic spots, onsen towns, and traditions long kept.

5. Kyushu- This place is so far from the rest of Japan that is developed its own Japanese culture. It is still Japanese but with a twist. There are a number of local delicacies and onsen towns. Though, all in all Kyushu is more for the more seasoned Japanese traveler.

6. Hokkaido- Like Kyushu this place is far off from the rest of Japan. Unlike Kyushu the native Japanese people (Ainu) were here plus the influence of Europe led to a weird mix of cultures. The distance from the rest of Japan means large expands of untouched nature. Beautiful lakes, forests, and walks await you here.

If you plan your trip to cover all 6 of these regions you should be plenty safe in being able to say "I've truly been to Japan!".
The regions you would not have gone to would be Shikoku and Tohoku. Leave those for next time. Okinawa is techinically part of Kyushu but is pretty far to get to. Nice for getting away from the summer heat though.

Lastly note that summer has plenty of events and festivals, and is Mt Fuji climbing season.