Kabuto Wins. Kusanagi's cutting power couldn't get past Kido's Webs- Doubt, Mere laser beams are gonna disintegrate it/pulverize it. Shinra Tensei, kinda, don't work against his body due to liquification. Gedo Rods, prolly, are outright useless given he possess 5 different entities to disrupt his Chakra (that's being taken control of by the Rods.) Sound Based Genjutsu, are cannonically proven to be thier weakness, so once caught they're done for, given Chakra Disruption through Rods aren't a viable counter to illusions, as shown in the manga.
CT would only be thier choice of winning, given all of thier prior powers are effectively countered. Even then - Manda 2 should crawl out of the core, from the satellite, saving Kabuto in the process. Muki Tensei should disrupt thier formation by converting thier rocks into, pointy staglamites, that rupture the orb when they connect.