Ahtrun's wounds opened again because he was'nt fully healed and also because of G-forces introduced by mobile suit suddenly accelerating and deccelerating. You can't work your body "at full power" when you aren't healed, because wounds might open and you are in trouble.
Athrun's fighting abilities at the moment are surpressed because of his wounds. He might be grounded for episode of two.

Kiras' "no kill policy" limits his abilities against Shinn, because he as to watch out not to aim for cockpit for instance... He essentially fights with one hand tied behind his back to speak literally.
Shinn does not has this limitation and also he knows that Kira won't go for a kill. So he has no worry about that. Meh, he was really surprised when he received point-blank railgun blast. [img]i/expressions/face-icon-small-happy.gif[/img]

Shinn also goes into blind rage when fighting which is a minus. When in rage you can't think clearly, of course you press on and on like beast but you completely drop strategy. When fighting Kira you need strategy - Impulse did beat Freedom only because Shinn and Rey analyzed Kiras' tactics and came up with a plan.

Ray looked extremely displeased when he saw SF. Kira wasn't that pleased to see Legend either.

Ray did not let Luna fight because he knew Shinn has feelings for her and he promised to protect her. Recall that in her first fight in Impulse Shinn blocked stray shot at her and told Luna that she's careless.
Having Luna arround while battling Kira would put Shinn in disadvantage beause he would keep an eye on her. You just can't devote yourself to a fight with Kira while also protecting Lunamaria.