Here's my write up for replacing blend door actuators:
That said, your story sounds a little confusing but it's possible one or both of the first two actuators mentioned in my write up may have stopped working.
DIY: Dash Blend Door Actuator Replacement 05-09 Mustang
In total there are four: 1. Floor/dash vent actuator on driver's side behind gauge cluster (Motorcraft part no. YH 1870). 2. Defrost vent actuator on passenger side behind the center console (upper) (Motorcraft part no. YH 1870). 3. Temperature blend door actuator on passenger side behind the...