I have a new to me 2011 convertible base V6 mustang. The rear windows are down and the top is down. The car seems to think that the rear windows are up so it will not raise the top. It also thinks that the top isn't fully open or closed and it won't raise the rear windows.
At some point it's...
You can put the top up and down manually fairly easily but you must first disconnect the hydraulic rams. There is a cover over the bolt held down by a t30 bolt, then another t30 bolt to disconnect the ram from the top on each side.