As for the Santa Rosa stub, I think you're right about the freeway being the end. That, and expansion of SRJC to include the stadium.

According to California Highways and Public Works, 1964-65 (p. 18), conversion of 101 through Santa Rosa to full freeway was completed in 1965. Of course, as with Stockton (99), where the last railroad crossing of the freeway didn't get removed until the late 1960s, it's not clear whether that included eliminating all railroad crossings - but it's likely that it did. So the rails still there when I lived there in the 1970s were just unsalvaged remnants from freeway time.

Also, when I lived there, the former NWP line still operated as far as the Sebastiani Winery and the old NWP station just north of downtown Sonoma - didn't get cut back to south of Napa Road until the 1980s along with a major road and intersection improvement project.