About 600 of a 1,200-mile tour from Baltimore, MD, to Davenport, IA, were on trails (BWI, Baltimore & Annapolis, and Washington, Baltimore & Annapolis trails in Maryland; the C&O and GAP to Pittsburgh, the Montour and Panhandle trails around Pittsburgh to Ohio; the Kokosing Trail in Ohio; and the Kankakee River, Illinois & Michigan Canal, and Hennepin Canal trails across almost all of Illinois. That route goes north of the route you’re considering, but it avoids the hills of southern Ohio and Indiana (there was only one day of significant hills in eastern Ohio). To avoid heavy traffic near D.C., we rode the Metro train from Bowie, MD, into D.C. I could have continued across Iowa from Davenport to Council Bluffs, much of the way on rail trails.
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. The 2,400-mile trail (I started in Kansas City) minimized hills by following rivers - the Platte and North Platte in NE, Sweetwater in WY, Snake across ID, and Colombia in OR. Numerous historic sites and landmarks line the trail. Wyoming is the only state where towns are widely spaced.
If you go through Missoula, there are about 150 miles of rail trails between there and Spokane, which I rode last summer – Route of the Olympian, Hiawatha, Coeur d’Alenes, North Idaho Centennial, and Spokane Centennial. Most of I-90 west of Missoula can be avoid by taking US-93, MT-200, and MT-135 to St. Regis, MT.
Some challenges on your proposed route:
The Katy Trail is a great ride, but from the trail north to Iowa is hill after hill after hill.
Yellowstone is a terrific park, but has narrow roads, lack of shoulders, heavy traffic, and significant hills.
Journals from riders on the John Wayne/Ironhorse Trail state that much of it is loose ballast.
If you’re interested in details of the routes I mentioned riding, contact me at firstname.lastname@example.org, and I can send you itineraries and journals of the tours.