A nice route west from Council Bluffs is to follow the Platte River to Kearney, NE, where the Oregon Trail route joins the river and follow the Oregon Trail to Portland, OR.
One thing to note if you follow the Columbia westward to the Pacific through the Columbia Gorge: The wind blows predominately from the west in the summer, creating quite a fierce headwind if you're heading westward.
Some challenges on your proposed route:
Journals from riders on the John Wayne/Ironhorse Trail state that much of it is loose ballast.
I got the impression that the OP will be heading west on the Iron Horse from Ellensburg WA to Seattle over Snoqualmie Pass. This is the well-maintained gravel section of the trail, and people regularly ride it on road bikes. The section of the John Wayne east of the Columbia River to the Idaho state line is the unimproved section that has loose ballast and closed trestles.