Unless I missed a new schedule, you will have to fly SFO-NRT then transfer to HND by the horrible bus or slightly less horrible train connection.

I can't see HND-CTS-HKG as a problem (unless CX drop CTS). You might be safer doing CTS-HND-HKG since JL now fly HND-HKG.

HNL appears OK so long as you use the QF flight (not JQ with a QF number) The risk is that QF may hand over the route to JQ then you are stuffed unless its ticketted.