Given that the Stun Removal skill explicitly lists modifiers for the number of stun rounds already, I would assume you are not supposed to also apply the maneuver penalty for being stunned. Also, the -50/-75 penalty for being stunned only applies to "movement and maneuvering", which I take as meaning actually moving around, not all "maneuvers" in the RM sense of skill checks. Most actions don't have a penalty because they are simply impossible while stunned; stun removal skill is of course an exception to that.