The abandoned line parallel to 202 N of West Chester is the PRR Frazer Branch (ex-West Chester RR), which ran from West Chester to Frazer. It was abandoned in 1932. I suspect the line that served Downingtown Paper was either the RDG Chester Valley Branch or PRR New Holland Branch; the P&T Branch skirted around Downingtown to the south, and I'm not sure it actually had any freight sidings on it.
The Trenton Cutoff (Morrisville-Glenloch), P&T (Glenloch-Thorndale), and the Atglen & Susquehanna (Parkesburg-Wago Jct.) were built as part of the PRR's Low-Grade freight line program. (Actually, the Trenton Cutoff was built slightly prior and realigned a little as part of the program.) These lines had low grades and few curves, necessitating extensive cutting and filling, and were intended more or less exclusively for rapid movement of heavy freight trains, relieving congestion on the Main Line and reducing the need for helpers. As I said, the P&T was conceived of as part of a larger project, never completed, to avoid grades on the Main Line from Philadelphia to Glenloch, but it also allowed freights to bypass the climb out of the valley of the East Branch of the Brandywine at Downingtown. The line connected to the Trenton Cutoff on the north side of the main line at Glenloch and kept its elevation as the main line descended towards the Brandywine. The jumpover at Whitford allowed the P&T to maintain its elevation on the flank of the South Valley Hills, although immense fills were still required. ("Triumph III", if I'm not mistaken, has some impressive photographs of the construction.) West of Downingtown, the P&T converged with the main line again and entered Thorndale Yard via a classic PRR flying junction, terminating as #5 and 6 running tracks at Caln.
The line was 12.72 miles long, according to PRR track charts, and more or less all of it heavily engineered. And if you think that's cool, check out the remains of the Atglen & Susquehanna: running through more or less the middle of nowhere Atglen-Quarryville-Safe Harbor, with absolutely *colossal* fills, cuts, underpasses, and so forth. (If you turn onto Pennsy Road and go west, just north of Quarryville, you may not realize that the hill on the left-hand side is all a fill until the road ducks through the stone tunnel under it--I didn't.) There are also impressive high bridges, as on the P&T at Downingtown, at Martic Forge and Safe Harbor.