Tokyo - Kyoto - Koyasan - Osaka

Hi there!

That's a great plan there! Especially Koya-san is lovely to spend the night at with your loved one.
Looking at the JR Pass versus normal tickets, I would suggest buying normal tickets as you go, because you simply don't do enough long distance travel to cover the price of the JR Pass. The JR Pass is really nice if you make some Shinkansen trips, a return trip Tokyo - Osaka already pays for the pass but it would not be the best buy since you only go one way.

As for the first night, why not book a hotel close to the Airport and travel on the next morning to Tokyo city, this way you can relax from your long flight and begin the next day well rested. This way you also avoid the chance of being stuck on the airport if there's a flight delay.

I hope this helps!
Daniel

Thank you Daniel! :)