I think the OP's best option is to either:

1. Change your reservation now since it's a net cost savings even with the change fee.

2. Do not touch your existing reservation and book a separate one-way to the west coast. I've had similar overlapping bookings on two occasions, booked months in advance, with no problems. Officially, you are supposed to fly what you book. Still, what businessman has not changed flight plans mid-trip? Happens all the time.

Either way, spouse will probably keep E+ unless something like a schedule or aircraft change makes Delta's computer auto-reassign seats.

On a side notes, I've been sorely disappointed by the uselessness of RUC's. Either the upgrade clears withhout them on "easy" routes, or there are hardly any seats available hub-to-hub after Delta monetizes the first class cabin. RUC's are great for LAX/SFO-JFK flyers, though.