A look at population density suggests a preliminary check:
Approximate time estimation for the Natron Cutoff
In southern Oregon, most people are living near the Applegate Trail, on which settlers arrived since 1846, and along the original railroad track. The town of Medford, largest in Southern Oregon, came into existence by decision of the railroad, to cross the Bear Creek at a certain location. When the Natron Cutoff was finished, Southern Pacific did not have this kind of influence any longer.
Only one city is connected by the Natron Cutoff: Klamath Falls with 21000 citizens. This situation is enough reason for a preliminary check, how much time the trains will need between those areas, that allow to expect a considerable amount of passenger exchange en route. On the southern side, this area extends to Redding (81000 citizens), on the northern side, to Eugene and Springfield (182000 citizens summed up).
The Natron Cutoff was built less steep and curvy than the old alignment, but nonetheless, it is a steep and curvy mountain route, mixed with some fast stretches. Chico - Dunsmuir will be used for comparison. As with any rough estimation, there is a considerable margin of error. Pessimistic and optimistic estimations are going to mark this range.