The Second District of the AT&SF
This line was built by a predecessor of the Santa Fe in the late 1800s. It was part of the "passenger main line" (Second District) between Los Angeles and San Bernardino, via Pasadena, until the late 1960s. At that time, I-210 was built a few blocks north of the right-of-way through Pasadena, and the main line relocated to the median of the I-210 freeway.
The original main line left behind by the 1960s freeway relocation became a spur, joining the "new" mainline at a flyunder junction in the freeway median (photo below). This spur served lumber yards and small businesses in East Pasadena and Lamanda Park, but it was abandoned in the 1980s.
The Santa Fe routed most of its freight through Fullerton; the line through Pasadena was used for passenger trains and a few piggyback trains and locals. The portion between Los Angeles and Pasadena is scenic and winding, but not really suitable for fast freight. Amtrak ran both the Southwest Chief and Desert Wind over this line, but relocated the Desert Wind to the Fullerton Line in 1986. When Santa Fe abandoned the route between Los Angeles and Arcadia in 1994, Amtrak rerouted the Southwest Chief through Fullerton also. Except for a short re-routed section near Union Station and Chinatown, this former Santa Fe line re-opened as the MTA Gold Line Light Rail service in July 2003. The Arroyo Seco bridge, midway between Los Angeles and Pasadena, was retained and double-tracked.
See also The Pasadena Branch.
Why would they abandon the old way through the city for the main highway, what with the now-gone flyover near the eastern line terminus.
I looked on Google Maps and it appears that the former railroad bridge shown in photo nine is actually part of a driveway for a distribution center. God bless.
It seems that at E Glenarm St an abandoned RR junctioned from South Pasadena to Mission Road
this line isn't technically abandoned it is still in service, in some certain section such as the spurs are abandoned.
"It seems that at E Glenarm St an abandoned RR junctioned from South Pasadena to Mission Road"
Jonathan, look up SP Alhambra - Pasadena
As of October 2014, the original, abandoned, single-line steel overcrossing at Huntington Blvd and 2nd St in Arcadia, and a similar overcrossing spanning Colorado Blvd west of Santa Anita Blvd have been refurbished and a second line added to accommodate the future extension of the Metro Gold Line light rail from Pasadena to Azusa. The old at-grade crossing, rail, and bed at Santa Anita Blvd was removed and replaced with an overpass and new approaches just east of the new/old Arcadia station (original building located at the LA County Fairgrounds). Most other original at-grade crossings in Arcadia and Monrovia have been upgraded, but otherwise follow the same path as the original SF bed.
did the santa fe railroad ever parallel siera madre blvd in pasadena?
The tracks never paralled Sierra Madre, those tracks were the PE Sierra Madre Line with a crossing at Walnut. There were also several otter lines in East Pasadena, including an line up Rosemead that might have been SP or PE. also a strange cutoff build in the early ATSF days but removed before 1900, I believe.