Maybe, if you explain your plans a little bit more clearly , we could better assist. Because right now all I can say is if you're flying out of LAX, someone will issue you a boarding pass for your pending flight. For other flights you may be connecting to, I'm

.
E.g. What's your connecting flight, and how much connecting time do you have? How much time do you have remaining at LAX and are you airside, and can get landside? (I'd not do that, but the JL counter is in TBIT iirc.)
Other than that, I'd trust what the counter and Flagship Lounge and EP lines in that they apparently are incapable of enabling your future boarding pass(es) for your flight out of. NRT. If JL is the ope rating carrier, they will have to reaccommodate you if you miss your flight, regardless - and JL is pretty good about reaccommodating distressed travelers.
Good luck with your travels!