Don't ride to Baker City. It's further - plus there are no two-lane roads you can use, thus forcing you onto I-84 which sucks. From Ontario take US 26 West to Bates - which is the connecting point for the TransAm.
As for the latter part of the trip - if you do the coast, you should ride north to south - wind issue again. You can ride north, but you'll be fighting a stiff wind most of the time. Plus 101 has a lot of traffic - good shoulders, but traffic. Best stretch is Lincoln City to Florence heading south. It's also really nice near the Calif border, but that's way out of your way.
Generally speaking, you will be heading INTO the direction of prevailing winds all the way to Portland. By staying in the forests and out of exposed areas you reduce the risk of having bad headwinds - but there are no guarantees in cycling.
Are you doing a round trip? If one way, why not send your bike there and bike back???
Best - J