Most of the site, including the R3 bunker was sold off in 2006/7 (the current 'for sale' signs have nothing to do with the MoD). A few of the buildings on the site including the R30 and the T84 Radar still belong to the MoD as part of the Remote Radar Head. It is most likely the MoD forcing the museum trustees into paying for the land instead of gifting it, However the R30 and T84 have preservation orders on them, hence anybody who buys them can do nothing with them.
One other thing to note is the place hosts a quite big collection of stuff from RAF Coltishall.