Based on my understanding of how things work, you should be able to check bags all the way through to KUL. As you say, the gap btwn flights is less than 24 hours. What's more, JAL and AA have very well established operations at NRT and they work together as alliance partners.

However, if you've discovered a thread where someone with direct, recent experience of this scenario is having difficulty checking luggage to his/her final destination, I can't deny the possibility that the situation has changed since I last looked into this. If you want to point us to the source of the information that's clouding the issue for you, people on this forum may be able to clear things up.