I ma not a runner but your planned route has some very rocky sections including the infamous PA rocks. There are a lot of runners in the whites that have no issues with rocks, but they tend to be stationary. PA rocks seem to be "bred" to be unstable leading to very unstable footing no matter what speed you are running. From Southern PA to WV (really to Springer), the trail is predominately old woods roads so I expect you would have no issues with your mileage assuming the PA, and to slighly lesser extent NJ and NY rocks dont cause an injury.