I think the assumption was that Zodiark just needed to be strong enough to break his shackles on The Source as Hydaelyn's strength was already waning, and then after that it's just a matter of ferrying him around to the rest of the shards, including The Thirteenth so he can get the rest of his guts. Or even just bringing the rest of his guts to him from across the rift. After that he would be fully formed, and strong enough to rejoin the rest of the shards himself.