I've ridden across Nebraska many times - 1st time on Hwy 2.
US 26 / US 30 ain't exactly the most scenic -
But you want to retrace a specific route which, not surprisingly,
became a major transportation corridor - trail/railroad/highway/interstate.
The section between Kearney and Marysville can be very pleasant -
Provided you stay off the US highways as much as possible.
In Nebraska Hwy 74, Hwy 4, and Hwy 8 are all quite nice with low traffic.
North-south highways have more traffic than east-west ones - esp. US 81 and US 77.
Diagonal roads in the Great Plains are very rare.
You will have to zig and zag to follow the actual Pony Express route.
There is a short section of unpaved road between Powell and Fairbury
Which follows the Little Blue River - then Hwy 8 goes on to Rock Creek Station.
Old Highway 36 in eastern Kansas is great for cycling -
But the stretch between Marysville and Hiawatha has pretty heavy traffic.
Most of it has wide shoulders, but about 20% does not - narrow & gravel.
Plus the the topography is rolling with limited sight lines.
Traffic map for NE:http://www.transportation.nebraska.gov/maps/Statewide%20Traffic%20Flow%20Maps/2012-Statewide-Traffic-Flow-Map.pdf
Traffic map for KS:http://www.ksdot.org/burtransplan/maps/CountMaps/Districts/count12.PDF
Fun image from Google in southern Nebraska: