When I double checked this it looks like my tickets were issued twice (so 2 ticket numbers), but I clearly remember applying for the upgrade waitlist after the first one was issued. (Question: Is the AsiaMiles site smart enough anyway to disable waitlisting for a PY->J upgrade if it can tell that you are only on E fare?). On Manage My Booking the outbound sector already says E class.

I guess if this falls through, I'll also have Instant Upgrade to try at the airport.