AS doesn't fly ORD-JNU anyway, so you're likely to fly AA ORD-SEA and connect to AS for SEA-JNU. This leg is less than a 2 hour flight, so it's probably not worth a lot of hassle trying to score a F upgrade. Use your miles to go F from ORD-SEA, if you care enough about F to blow miles on the upgrade.
Enjoy Alaska and take lots of money... it's expensive!