Sorry to hear about your bad experience!
fwiw, in the last couple of years I've traveled ORD-NRT-BKK on JAL in F and J on award tickets and never had anything less than excellent service. Lounge escorts, personal greeting from the purser (in F), personal greeting from my FA (in J), good food and wine, etc.
The last time I was was in F ORD-NRT I was the only W/M in the cabin and was treated just about the same as the big shots who seemed very familiar to the FA's. Maybe a little less personal conversation and chit chat, but I believe that's down to a language issue.
Seems like you may have had a really bad crew, or someone very, very important was on your flight and you suffered for it. In the future, keep in mind that the FA call button on JAL is really to call the FA's. It's not an emergency alert button that brings a scowling FA, like on AA or United!
Hope your next flight works out a lot better!