Looked long and hard for an accurate set of instructions on how to do this.

DIY Convertible Top Cylinder Replacement (and rear seat removal details) | Mustang Forums at StangNet

The instructions also show the hydraulic pump. If you need to replace that, the only things required are to pry the pump base from the floor bracket with a flat blade screwdriver, disconnect the electrical connector and disconnect the hydraulic lines where the flare nut on each T fitting screws into the pump housing. Replacement pumps come with new rubber mounting plugs; just push in the center with a blunt ended round tool and pop each one into the floor bracket.