After 20 minutes on hold, I got through to the India call centre. Much to my surprise, she was very helpful and fixed the problem in just a couple short minutes.

After all that headache, the website will no longer let me purchase the economy plus upgrade (even though it offered it 8 minutes ago), but it will allow my wife to when I log in to check her in. Unless they still have upgrade seats available at the airport tomorrow, we are stuck in awful seats pretty well the whole way back.

Teaches me for booking a crappy routing to save 20k points.