Need help organizing our days

Hi everyone, I am surprising my fiancée in March with a trip to Japan for her birthday. I've been once before and have a general idea of the basics. I know the gist of where I'd like to take her in each city, my struggle is in what order I should structure the days of our trip. Her sister may join us in Tokyo somewhere in the middle, but she is only interested in Tokyo.

We fly in/out of Tokyo and have 10 full days not including airport travel. The plan at the moment is to spend the bulk of our time in Tokyo and at least 3 of those days at Tokyo Disney. Kyoto for 2-3 days, and day trips to Nara, Nagano and Fuji Five Lakes if possible. My gut feeling is to do Kyoto/Nara in the beginning and save Tokyo/Nagano/Disney towards the end. Fuji Five Lakes isn't a must do, but it would be nice if possible. We'll also have the 7 day JR Pass to get between cities.

Any input or suggestions on how you'd organizing the days would be appreciated.

Thank you!

With only 10 full days. I would drop Nagano.

Concentrate on Tokyo and Kyoto.

Day 1-5 - Tokyo, including Fuji 5 Lakes day trip etc.
Day 6 - Travel to Kyoto in morning, sightsee in afternoon
Day 7 - Day trip to Nara.
Day 7-9 - Kyoto.
Day 10 - Return to Tokyo

depending on your flight time, you may be able to may returning to Tokyo the day after, giving you one more day for Tokyo or Kyoto.