Now it finally shows up on AA for a decent price. $727 on AA.com; Fare Code: N; use Google Flights for flex dates; 18,349 EQMs; 3.9CPM; see below for AA itinerary; only book on AA.com!

American Airlines
5954
Operated by Compass Airlines As American Eagle
San Diego (SAN)
October 9, 2015 09:35 AM
Travel Time : 0 h 53 m
Cabin Class : Economy
Seat : unassigned
Los Angeles (LAX)
October 9, 2015 10:28 AM
Booking Code : N
Plane Type : E75

Japan Airlines
JL 61
Los Angeles (LAX)
October 9, 2015 01:20 PM
Travel Time : 11 h 35 m
Cabin Class : Economy
Seat : unassigned
Tokyo (NRT)
October 10, 2015 04:55 PM
Booking Code : N
Plane Type : 77W

Japan Airlines
JL 729
Tokyo (NRT)
October 10, 2015 06:55 PM
Travel Time : 8 h 5 m
Cabin Class : Economy
Seat : unassigned
Jakarta (CGK)
October 11, 2015 01:00 AM
Booking Code : N
Plane Type : 788
Flight Depart Arrive

Japan Airlines
JL 726
Jakarta (CGK)
October 11, 2015 09:55 PM
Travel Time : 7 h 30 m
Cabin Class : Economy
Seat : unassigned
Tokyo (NRT)
October 12, 2015 07:25 AM
Booking Code : N
Plane Type : 788

Japan Airlines
JL 66
Tokyo (NRT)
October 12, 2015 05:25 PM
Travel Time : 10 h 5 m
Cabin Class : Economy
Seat : unassigned
San Diego (SAN)
October 12, 2015 11:30 AM
Booking Code : N
Plane Type : 788