Glad you found what you needed. On separate itineraries, you will clear separately - you at your window, and her no more than 24 hours before departure. If you were on the same reservation, you'd both clear (or not clear) together.

As far as what DL.com might not be able to answer for you, if you get the upgrade and your wife doesn't, you can just give it to her and take her seat in back, or ask the GA to give it to the next person on the list (though if it's a full flight, your old seat next to her might already be gone).