Thank you, solid insight. It’s not gone - I booked a different itinerary fine at approx 1750 usd - but It seems those flights stubbornly show up in Google Flights, ITA Matrix and all Expedia backed OTAs. Attempting to check out fails.

I can’t price JL12 anywhere near a double stopover US itinerary so I wish those attempting it good luck. Adding a West Coast stop seems to work great if you want to get the OPs pricing; also taking AA across the Pacific from TYO. My tickets were JL coded and payment (used OTA) went to Japan Airlines.

edit: FWIW on AA you can get DFW in the mix at low price fine but I can’t get under 3.3k with JL A350 to DFW. C’est la vie.