WAS to ANC, ANC to Juneau, [cruise], Sitka to Seattle, Seattle to WAS
Hmmmm. I am doing an upcoming multi-stop trip booked with a companion cert: SEA-DFW, DFW-(via SEA)-LIH, LIH-SEA. But, I don't have an open jaw or a stopover in there (there is a forced overnight in SEA on the DFW-LIH leg, but that's not a "stopover").
It's not clear from your description, but it seems like you want to stopover at ANC, then open jaw between JNU and SIT, then possibly stopover at SEA. While this is bookable in a single AS itinerary, probably priced and sold as multiple one-way tickets, I don't know whether the companion cert has more limited routing rules.