I called EP desk again to try my luck. A competent agent was able to apply the SWU. But she said this ticket could not be reissued as RTW desk didn't allow it. Instead, they would grant the SWU by notating on my PNR, but I would have to stop by JFK ticketing counter to pick up the BP and she said this is called a 'grab and go' in AA speak
Knowing this is AA, I'm not exactly confident/will remain cautiously optimistic. I can't see for sure on tripcase as AA shut it down as you may know. But so far checked my PNR on CX/QR/AA websites and all show confirmed in First (A), did seat assignment and EF shows my J seat released with F seat taken, I hope these are signs that it worked. Oh well. This could be interesting..