If you are stopping in NRT for a few days, you wouldn't be considered traveling on a 'through' flight. You would do the normal routine of checking in at NRT before your flight or online if that's an option. The problem with HKG is that you have to have a boarding pass with a seat assignment to clear security and immigration whereas in NRT, you will be let thru with a standby boarding pass and issued a seat at the gate. Since you work for US, you would be eligible for a ZED LOW fare on JL.