RE: bike box
I heard some riders are shipping their bike box from Seattle to somewhere (e.g. bike shop) or someone (e.g. friend) in San Francisco, CA and then taking an airplane back home.
Amtrak
I've booked Amtrak Roomette back from Emeryville, CA to Seattle, WA. After looking at my options, this was the simplest for me (to get back to Seattle). The reason I'm starting from Emeryville, CA is because I couldn't add the bike for the Amtrak chartered bus trip from San Francisco to Emeryville. After checking around, I'll be taking my bike and person using BART from San Francisco to Emeryville.
Note: I'm doing the pre-ride.
Most Amtrak trains have bike hooks on the wall for 10 bikes in the luggage car which are reservable when booking the passenger ticket - this option does not require purchasing a separate cardboard bike box from Amtrak. I'm not sure if the hooks are usable for tandem bikes and have no experience with tandem bikes on Amtrak. Perhaps the staff at the stations could confirm options available for tandems.
I've used the Amtrak Roomette once from Klamath Falls to Seattle after Craters 1200 and many times business class from Portland to Seattle, all with a bike (and bike fee). All times have been the first train out of the station in the morning. The roomette from Klamath Falls to Seattle was a treat with 3 very good meals included. It was a good way to relax after the bike ride, eat, sleep, and enjoy the scenery.
cheers,
Mitch
RUSA 9700