You can also continue from the Portland train station to Astoria on the Amtrak bus, and skip the ride from PDX over to the coast. There are several motels and B&B's within a short distance of the bus station. It would allow a good night's rest before setting out, and an extra day on the coast.
As the others have said, boxing is not a problem.
Enjoy your ride, ride safe, and welcome to Oregon
From the FWIT Department: This is how we handle our gear on trains and planes.
The big yellow bag is a lightweight ripstop nylon duffle bag. All the contents of the panniers go into this bag. and the empty panniers go in the bike box with the bike (there is a lot of room). This leaves only the duffle, the rack pack and the handlebar bag to manage rather than 4 panniers, rackpack, and bar bag. The bag looks fragile, but it has been checked as baggage on several flights, and is still intact. Packing for the train is relatively easy, planes are a little more challenging.
Amtrak boxes, with the 3 pieces of luggage apiece to manage. Empty panniers shoes and helmet are in the boxes. My wife's duffle is black. She got hers at REI. The bag, 5 ounces, is carried in one of the panniers for the return trip home.