Miho Museum

Hello Scott,

Coming from Naoshima, the first part of business is taking a ferry to Uno. From Uno, the JR can be used to Ishiyama station (it's actually very close to Kyoto station). From Ishiyama it's a 50min bus ride to the museum. Here is the bus time table.

The Ferry time table Naoshima - Uno is here.

Lastly, the JR Route Uno - Ishiyama. Route 2 and 3 are the best.

I'd take the ferry from 7:50 am which arrives 20 minutes later. Than use route 2 or 3, departing Uno station from 08:29 arriving at 11:20 at Ishiyama and then the bus departing at 12:10 to the museum. The connection from train to bus is 50 minutes apart, you could also spend 20 minutes or so at Kyoto station, get some nice food at travel with a later train to Ishiyama.

From return to Tokyo, travel back to Kyoto station and take a Shinkansen directly from there to Tokyo.

Hope this helps,
Daniel