I missed that this was an award flight. If you kept the story to AA simple, such as ... we had booked a J ticket award and because of a maintenance delay, we lost J on our connecting flight and flew coach. As such, we would like to get the mileage difference returned to my account ... I think you could get an easier resolution. Not being able to sit together is an inconvenience (and more in your case) but not something that will be seen as a quick and easy resolution. It's important to pick which issue is most important to you and focus on that one.
I do think that under these circumstances someone might switch. Did you either of you bring this to the attention of the flight attendant?