[Troo]

The majority of staff at ryokan, minshuku, and so on do not speak English (or, at least, not terribly well). There are also many of these places who will not accept foreign guests without a local to vouch for them.

Book in advance before you go.

You're also going at possibly the worst time for finding accomodation. Golden Week starts on the 29th of April, and while it technically ends on the 5th of May, hotels and travel can be a pain in the bum for a few days after. You really should've booked this by the beginning of the year to stand any chance of getting your choice of accomodation.

You'll do better if you book whatever you can get up until about the 8th, then hunt for more traditional options for the remainder of your time, as people will be back to work and rooms will be more available.