Have you added in extra time to acclimate to the higher elevation before the accent? You need to pause beforehand, so that you do not get elevation sickness.
My only experience with elevation sickness was in Santa Fe, New Mexico at the 10,000 Waves Onsen.
https://tenthousandwaves.com/ I had driven up to Albuquerque the day before, so I had a day, and was acclimated to the higher elevation. My wife flew into Albuquerque the following day, and we went to the Onsen, which is in the nearby mountains at 8,000 ft. We spent 2 nights each in the Sailor Moon and Blue Moon cabins.
We had scheduled one of the private baths for the first night, and it was wonderful. There was a light snow at that time, so we had the Hot Springs Experience during a snowfall.
After our initial private bath, my wife came down with a headache, which is one of the symptoms of elevation sickness. She missed the morning massage the next day, and I ended up bringing her breakfast, lunch and dinner to the room. I want to stress that she only got off the plane from Los Angeles (sea level), and did nothing but sit in the car. Her only activity was to the take the luggage from the car to the cabin, and to eat a meal.
She did get better, and the following two days were wonderful.
You are probably planning to go from Tokyo, which is basically sea level, and go up to station 5, and then you are planning to start hiking up the volcano. Please give yourself some time to acclimate, and acclimate your body to rarefied air, before starting the accent.
http://fuji.yamaiko.com/en/plan/sickness.phphttp://www.japan-talk.com/jt/new/6-reasons-you-might-not-enjoy-climbin...The best prevention is acclimation, or just spending several hours letting your body get used to the thinner air. Many of the stations have bunks, and you can just take a nap. After all, you are going to be climbing during the evening, and not sleeping.
Good Luck, in planning your vacation.