If you are picking JAL they also off a paid upgrade to their PE at the airport even if you are booked on the AA flight numbers.
JAL website:
http://www.jal.co.jp/en/info/inter/130712.html
I did this earlier in the month on NRT-JFK (JAL 787) and ORD-NRT (JAL 777) and with no aisle or exit rows available in Economy it was definitely worth it. You also get Admiral's Club access in ORD via JAL.
In ORD you need to go to the JAL gate (K17?) and they will process the upgrade there. It was JPY 30,000 in NRT and $USD 300 in ORD, flight was ~12-13 hours I believe.