In 1963, an AN/FPS-35 was installed as the primary search radar, and one of the AN/FPS-6 height-finders was replaced with an AN/FPS-90.
The following year, however, the height-finder was again replaced, this time with the AN/FPS-26 to replace the remaining -6. That winter, a major storm would cause the antenna of the FPS-35 radar to topple. It was not until the following year that it was replaced by the antenna from Manassas AFS. Search functions were carried out by a temporary installation of an AN/FPS-64.
In 1966, a Burroughs CSA-51 computer system was installed. Various other modifications and upgrades were carried out over the years, but with the reduction of the threat of bomber aircraft, many of these stations began closing.
Fortuna AFS shut down operations in 1984.
Update January 17, 2020:
Some time around 2016, almost all of this base was demolished except the the FPS-35 radar tower. It is being kept by a mobile service company
Coming around the corner, the open, barren landscape makes this place obvious to all who pass. The highest point in an otherwise flat state, the hills here have no vegetation save for a handful of smallish trees.
The site has been largely gutted of anything that could be sold off for cash. Even plates of metal from the walls of the towers have been removed.
The design and layout is quite familiar to anyone who has explored any radar site in North America. I was disappointed to not be able to get up the 35 tower. I have encountered only three so far, and not been able to climb any of them.