Posted too soon!
I get the rail passes here:
www.japan-rail-pass.co.uk/
They supply pocket wifi and Suica cards as well. They also sell a service whereby you can call an English speaking helpline at any time but honestly you won't need it.
I don't buy the business class because being used to British trains then standard class seems pretty damned comfy! Power supplies and plenty of leg room at each seat usually. If you go Green class you do also have to book seats in advance whereas for regular class you can book but most trains have some open seating. Booking seats is easy - you can do it at the stations, again using the medium of Google Translate to help.
This app is free:
[https://www.navitime.co.jp/pcstorage/html/japan_travel/english/]]
And really useful - you can plan your journeys on it, you can tell it to give you a journey covered by the rail pass and it also has current information on eg line closures due to local problems. Its also useful to take into the booking office to show the route you want.
As said upthread, Ryokans can be booked online. Meals in Ryokans are usually set meals but they will cater for dietary needs (I'm a veggie, this wasn't an issue for them). There are also some nice Japanese small hotels which are Japanese style, have Onsens etc but are not full Ryokan.
I agree with the advice to get a guidebook, read some blogs, see what appeals to you and then just book it yourself along a logical route. Autumn colour is probably slightly cheaper than cherry blossom time and may not need booking so far in advance.
If either of you are veggie/dietary restrictions I'd also recommend the HappyCow app - its very useful to help find food outlets which cater for veggies/vegans and allergies.
Come back to the thread when you have some places in mind!