the heck does healing have to do with your body still being hurt and beaten. Your body is still bruised and battered after each healing , and you need more time to rest to be completely healed again. Sasuke was already healed and rested with an upgrade.Naruto wounds healed and his chakra was increased before he went to Kimimaro. So that's invalid.
Also after Sasuke chidoir'd him he healed again and his charka was back.
Same goes for Sasuke when he went curse mark. They were equally healthy, with naruto having the advantage.
Naruto was beaten badly by Kimimaro since his clones were constantly defeated and Naruto would feel the effects of the damage inflicted on them with his real body. He had become exhausted and in pain again by time he met up with Sasuke after running him down again.