This is likely the wrong end of the Prairie Spirit Trail for you, but here’s the route that I recently took from Clinton to Iola, over two days. Camped at the Osage Prairie RV Park in Nevada. The stretch between Nevada and Appleton City is fairly long with few services, but the route otherwise has fairly well-spaced options for restocking on food and drink. Mostly flat, with a few hills near Uniontown KS. There is about 2-3 miles of gravel road just south of La Due, otherwise all paved, with low-to-moderate traffic levels, and decent shoulders where there is traffic.
Alternately, here’s a route between Ottawa and Clinton, via the Flint Hills Nature Trail: http://ridewithgps.com/routes/9284291
Camping at La Cygne City Park, or Linn County Park. There *may* be construction on MO-18 west of Clinton. I saw “road closed” signs when I was riding that way, but don’t know precisely where the road is closed…