I agree Japan is easy to manage.
Let us know how many people in your group, and age range?
It is more of a eating trip? shopping trip? sight seeing trip? how many days?
What do you want to see? what to eat? Places you want to visit, hot spring? theme park ?
If you are traveling around 本洲 and with senior, then I would suggest you join a tour.
Rushing on and off train to different cities with senior, just not a good idea