Bruce,
You mentioned the San Joaquin and Sierra Nevada.
The gauge conversion was later than the Wikipedia article would have you believe. The SP kept the SJ&SN narrow gauge until the traffic crunch in Nevada on the Carson & Colorado during the "Tonopah boom." The SJ&SN was then converted to standard gauge so that the cars could be sent over to the C&C. The need for cars in Nevada also accelerated the gauge conversion on the South Pacific Coast.
So much freight was headed down the C&C (acquired by the SP in 1900) to Sodaville or Candelaria for transfer to wagons to go to Tonopah (this was before the completion of the Tonopah RR and the eventual standard gauging north of Tonopah Junction and of the TRR) that the resources of the C&C was over taxed that the SP sent over locomotives and every available passenger and freight car.
At one time, the newspapers reported that there were hundreds of standard gauge cars on sidings across Nevada waiting to get to the transfer facility at Mound House (and that moved south as the gauge change progressed). The line was so overwhelmed that the railroad at one point embargoed all shipments except clothing, foot wear and food -- if you wanted to ship in mining equipment, you had to transload it to wagons off the standard gauge and haul it that way to Tonopah.
Also, I believe that I recently heard that the General Mills plant at Lodi closed and the operation on the remaining part of the old SJ&SN has now ceased.
Brian Norden