Half-width vs full-width refers to different types characters used in CFK languages (the explanation is long and involved, so I refer you to
Wikipedia).
However, I don't think that's applicable in your case. Have you tried calling JAL (or your travel agent) to input it for you? To be honest, it's not really a big deal -- they'll confirm your passport details again at check-in -- so I think you're right in waiting until you get to NRT to do so.