Most of my travel is business booked via AMEX Corporate Travel and I've used just about every upgrade instrument on these reservations, so long as the booking class is correct (not Q or O for India). Make sure you use the AA record locator and not the AMEX/Galileo record locator when you call AA.

The only caveat is I've always had to wait for a reservation to ticket before waitlisting/confirming upgrades, although I think others have more success at this than me.

40k miles + $350 each way is quite expensive though! Might as well toss in a Plat Challenge while you're at it