Never trained in Japan myself, but have a friend who lived in Japan for 5 years and studied Aikido the whole time he was there. He lived in Osaka and studied with the JAA. Whereabouts in Japan are you planning to go?
There are still quite a few Koryu schools in Japan. Bear in mind, what you call Jiu Jitsu is likely to only be part of a classical Japanese system, as "Ju Jitsu" usally refers to the unarmed section of a system. Many Koryu arts spend quite a bit of time on working with weapons.
As for finding them, that's easy enough if you know where to look. One thing I would say is that you need to be careful about asking to join a school. Some of the old fashioned schools in Japan don't accept just any old student. It's not like a karate class in a local community centre where you just turn up in your sweats any time you like!
Antonino Certa, in his book on Daito Ryu, stated that he had to get a letter of recommendation from a senior figure within the Aikido community in his country to present to the Daito Ryu head dojo in Japan before he trained. Mr Certa was already a black belt in Aikido before he went to train in Japan. Even with his experience and letter of recommendation, it took a few weeks for the Daito Ryu Dojo in Japan to accept him as a student.
There are plenty of "Gendai Budo" readily available in Japan. You would have no trouble finding an Aikido, Judo, Kendo or Karate class willing to take you on.
If you know whereabouts you're going it might be easier to point you in the direction of a school.
"Let your food be your medicine, and your medicine be your food"