I have been studying the history of the Pennsylvania Turnpike since 1995. The history is very deep. It goes well beyond the 1939 survey done by the turnpike.
It actually goes back as far as the 1820's. It was originally to be a railroad route between Harrisburg and Wheeling, WV. That was changed when Andrew Carnegie visited William Henry Vanderbilt and suggested that he discontinue surveying the route to Wheeling and instead offered to pay for the route to be changed to have it end in Pittsburgh, better yet Port Perry, Pa. 11 mile up river from Pittsburgh.
As for the railroad in the area which you walked in Fulton & Bedford County, There is amost half of the grade still visible in that area. It is either on the turnpike grade or on the area south of the abandoned pike roadbed.
The other interesting things in this area is the CCC camp which later for a short time became a Concentration Camp for German POW's.
I hope you become very interested in this area as I have of the whole South Penn right of way.
Enjoy and Yes If you want an escort, I would be happy to show you the sites in the Breezewood bike trail route.
Russ.