Jason,
If you haven't already seen it, try to find a copy of "Railroading in Eighteen Countries" by Carl R. Gray, (Scribners, New York, 1955). He was Director General, Military Railway Service, 1942-1945. His book has about 8-10 pages on the WP&Y in WWII.
It also has an interesting photo of a K28 on a barge leaving Seattle.
This is written from a high-level management perspective so there is little detail about operations.
Bruce Pryor