If you're trying to book that as one itinerary, it's not going to be eligible for a companion certificate. An open jaw or a stopover perhaps. If you want to use the companion certificate you'll need to deconstruct your itinerary. Someone like Missy could probably figure out how to get the most bang for the buck, certificate-wise; my head is spinning just trying to visualize where you're going.

One segment does jump out at me--are you sure the SFO-ORD options you saw at alaskaair.com were on Alaska and weren't AA code shares?