1) Part of the problem might not be that she didn't mind kissing you, but the location and situation.
Many Japanese women like stealthiness and privacy, especially with foreigners. It's best to take her to a semi-private and dimly lit place, where you can sit next to and hug her. Preferably a place with round tables (where sitting adjacent is easy), a booth, a couch, at the counter, etc... And it's best to take her to places that nobody knows her. Avoid her friends, co-workers, or her neighborhood on your private romantic date. Otherwise many Japanese women get overly paranoid that somebody they know will see them kissing.