Using Wounds
The wound penalty does not apply whenever the character takes any action. The player decides when it is dramatically appropriate to have his injury come into play. If the character takes the penalty due to his injury on an action in combat and fails at that action that he otherwise would have succeeded, he gains an Action Point. If he takes the penalty in a noncombat situation, or it negatively impacts him in a roleplaying situation, the character gains a Plot Point. The character can only gain one Plot or Action Point per encounter or scene. This isn't a free source of points, however. The character does not gain plot points by fulfilling his Motivation or playing out his Flaw, and does not receive any action points for completing Milestones or taking Extended Rests. The wound penalty can apply on any action the PC and player agree are appropriate to the wound.
The penalty could be a penalty on ranged attacks for injured eyes, on knowledge based skill checks for concussions, a movement penalty for leg injuries, Endurance penalty for bruised ribs, and so on. The penalties aren't fixed, any way the injury could hinder the player is fine so long as the DM agrees. The wound must prevent the character from succeeding or performing an action he would be able to if he didn't have the wound penalty. For example, he takes a -2 on his attack roll and gets a 17 total, when the opponent's AC is 18. The DM informs him that he missed and awards an action point. For movement based penalties, the character gains a plot point if the reduced movement prevents them from avoiding or making an attack.
The bolded part does seem to potentially cause problems. Essentially you can't get action or plot points the normal way once you're wounded? This could potentially be a very harsh penalty, especially at high levels when action points are more important. It might even mean that an irritating (-1) wound would be worse to have than a crippling (-4) wound, because the irritating wound prevents you from getting APs and PPs the normal way but is so small it is unlikely to provide many APs and PPs on its own.
This system might also lead to metagaming - players could intentionally put themselves into situations where their wounds would hurt them so that they can "farm" APs and PPs. This would be more likely with the bolded part because it means that doing this is the only way they can get APs and PPs.