I think my secondary ports are part way stuck open. How do I fix this?

 

Are you talking about an S5 NA engine's aux. ports? You can check the movement of the actuator rods by hand. This will give you an idea of how they work: http://www.aaroncake.net/rx-7/6porttest.htm

Keep in mind that the above guide is for S4 actuators, which move in the opposite direction of the S5 versions. S5 actuators push out to move the ports into the open position. S4s pull in.