I'll just tell you our plan later this year. Staying 2.5 days / 3 nights in Nagasaki. Get to Nagasaki 1~2pm the first day, few hours to take the family through a tour of the city (29 Martyrs real quick, then tram to Glover Garden, walk back through Dutch slope area down to Chinatown and over to Shianbashi/Kankoudori area). One full day for Haus ten Bos, another full day for Shimabara/Unzen. Not my first time doing any of this. But renting a car for the first time, for at least the Shimabara part. Not used to driving in Jpn, so I'm nervous about that. Thinking about squeezing in Nagasaki Biodome on the same day as Haus den Bos... that would then also require a car, and that might be too much in one day.

Does this tour let you on the island? This isn't something I would do as I'm just not at all into historical tours and such, but I know this is a big thing for many visitors and I'm really impressed that so many foreign visitors take such interest in Japanese history.