1. Cannot use eup on reward ticket.
2. If you eup from flex: make sure you have enough eup credits, and you need to pay $500 copay each direction.
3. If your wife ends up in economy, then she can always take your business seat from you and you take the economy seat.

Edit: also look at the price of a latitude fare, may be cheaper than flex +500 copay, but still no guarantee for upgrade before travel as you don't have a nominee spot...

2nd edit: as an E35k you might not have enough eup credits to upgrade your wife the entire round trip. You also don't have a nominee spot so you need to upgrade the day of travel since you are on different tickets.