If you are interested in connecting on CX, make sure you check the times of your arriving flight. Flights from JFK, DWF and ORD arrive in NRT in time to transfer to the CX flight to TPE, which departs at 1600. The flight from LAX doesn't arrive in time. I don't know about the SJC flight.

It's a matter of semantics, but JAL doesn't fly to Taipei; JAA (Japan Asia Air, a subsidiary of JAL) does. JAA offers four or five flights to/from TPE daily, none of which are AA codeshares to my knowledge. In addition, one has to allow extra transfer time at NRT to catch a JAA flight since it leaves from a different terminal than AA, requiring a wait for the bus. If you are flying in Y on JAA, you can still get 70% AA miles by booking in the correct booking class. (However, without exception, the miles have never posted on their own. I always have had to call AA and ultimately send them my boarding pass and ticket.)