I don't know about the Miho museum, but I've been to Meiji Mura and combined it with a visit to Inuyama castle and the Jo-an tea arbor, and altogether it took me the best part of a day. I started in Gifu and ended in Nagoya; coming from Kyoto will add a couple of hours. I used the bus between Inuyama and Meiji Mura and you could save quite a bit of time with a taxi.

Meiji Mura is a big place, with a lot of interesting buildings (e.g., Lafcadio Hearn's summer place, above a fish shop, a prison, an entire cathedral). You could just go see the Imperial Hotel, but you'd miss a lot else.

The hotel is at the far end from where you come in, so it takes about 30 minutes just to get there from the the ticket office by the bus stop. The map shows another entrance right by the hotel, so a taxi might save time there, too.