It was definitely not the Sound Nins' souls. I don't believe this counts as spoilers, but I'm new and so I'm not sure, so scroll down if you want to see why. Apologies if this is against the rules....

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In the manga, when the First and Second are defeated, their bodies simply disintegrate. Having the two Sound Nins appear from the ashes was a creative liberty the anime production team took--personally, I think it worked out quite well as it fueled the Third's anger a little bit more.

As for the others that were eaten as well, this of course raises two questions: 1) Do Kage Bunshins have souls? and 2) Why didn't the Third use another Kage Bunshin to attack Orochimaru?

My guesses are that 1) As Chakra is a described as 'spiritual energy' early on, it does have some soul-like components and 2) Because the Kage Bunshin would be weaker and require more Chakra, which he was running low on in the first place.

[edit]Sorry; I'm an idiot and forgot how to count Hokages....[/edit]