KCSM Naruto most likely wins. He was already superior to A's speed in KCM (and thus also significantly faster than MS Sasuke's natural speed), now he has the added boost of SM to counter Sasuke's Raiton Armor enhanced speed, considering that SM led to him being able to track and tag Juubito of all people. He can still anticipate Amaterasu attempts and either counter with his cloak like he has done in canon, or dodge, and arrows were already dodgeable in KCM.
At best Raiton Armor makes for a more mobile Susano'o. However Sasuke is still going to suffer from all the same drawbacks of using MS techniques due to not having EMS, and he doesn't have A's bijuu level chakra reserves to spam the armor and V4 Susano'o against clones that have the reflexes to dodge his attacks and launch nukes that could deal severe damage to V3 Susano'o, if not destroy it completely (Chou Rasenshuriken). Thus Naruto can wins either via outlasting due to having the better buff (SM, which he can extend by having a clone run off to gather natural energy), or spamming high power attacks (guided Rasenshuriken).