The South Penn was surveyed from Harrisburg (where it was to connect with the Reading) to Port Perry, PA, where it was to connect with the P&LE into Pittsburgh. No work was ever done on either the eastern or western extremities of the line, since this was relatively easy country and since the construction strategy was to get the heavy work in the mountains under way first. Much grading was done in certain areas between Blue Mountain and Donegal, including partial work on nine tunnels, before all construction ceased.
The original part of the PA Turnpike, between the Carlisle and Irwin interchanges, used the South Penn route, including finishing seven of the nine tunnels. But the highway actually used very little of the railroad right-of-way, since it could be engineered for a 3% maximum grade while the railroad was designed for a 1% ruling grade over most of its length. Thus there are many spots where a hard-core RR archeologist can find remnants of the heavy railroad grading. For example, the 10-mile eastern ascent of Allegheny Mountain, between New Baltimore (which was to become the South Penn's Altoona) and Allegheny tunnel was completely graded over a route that runs to the south of the present turnpike. Another interesting area is the wide northerly arc the South Penn made around Somerset, which included a large, partially completed fill over the CSX (ex-B&O) Johnstown Branch as Geiger Station, 3 miles north of Somerset. The CSX line passes under the fill in a still-existing tunnel, built for it by the South Penn.
The Wikipedia entry follows the common story, but actually there is no evidence that the PRR had any stock interest in the West Shore, which was promoted by George Pullman and others. Vanderbilt may have thought so, and it's possible that the PRR picked up West Shore bonds as a bargaining chip, after the NYC drove it into bankruptcy. But if so, that would have beenafter the South Penn was underway.
Also, Vanderbilt got cold feet part way into the railroad's construction and tried to negotiate with the PRR to take it off his hands. But since he had only 1/3 control of it, he had to get a decent price for his fellow investors, which included Carnegie and a lot of Pittsburgh businessmen. But the PRR wouldn't pay his price. This is what brought Morgan into the affair, and the famous voyage on Morgan's yacht was strictly an effort to bring the PRR to terms.
In truth, the South Penn didn't die after the agreement. The PRR was prevented from taking control, and the Pittsburghers tried to keep the project alive. Finally, in 1904 the B&O (which was under PRR control at the time) bought the property at auction and then split it with the PRR. B&O (under the name of the Fulton, Bedford & Somerset) kept the route between Mt. Dallas and Port Perry, and a Cumberland Valley (PRR) subsidiary took ownership of the route between Harrisburg and Mt. Dallas. Thus with the line under two different ownerships, it was effectively neutralized so that no future empire builder could make use of it as a through route. While the PRR made noises about possibly extending a line over their part of the route, I think this was mostly to avoid any legal problems. The split B&O (FB&S)-PRR ownership continued until the turnpike commission bought the rights and property.