Elfangor did know that Tobias and Ax would join up with other humans, but that still doesn't explain how he had enough time to prepare for it. From what I understood, after his deal with the Ellimist, Elfangor was immediately transported into his Andalite fleet against Visser Three to the night of the construction site.
The only explanation of the Escafil Device being in Elfangor's fighter at the time then be either a) the doing of the Ellimist or b) the rank theory, which I'm sticking with
No, no, that's what I used to think, but that's not what happens. First of all, why would he transport Elfangor thirteen years into the future (because he took him away from before Tobias was born, but the construction site battle is thirteen years later.) Besides, it was a different battle altogether. He came back, announced himself as Aristh Elfangor, the andalites reacted with a 'WTF are you doing here?', and he saves the day by ramming the blade ship. He beats the odds and survives, and then another Dome Ship, the GalaxyTree I think, exits zero space and rescues him. Elfangor talks to some captain and spills his whole whacked out story (aside from the location of the Time Matrix). He gets promoted to warrior and someone tells him that he'll be a prince in no time at all.
So, the Ellimist takes him to the battle he should have been in at that moment.
Now, as far as why Elfangor had an Escafil Device...I have always wondered about that too. My theory.
Elfangor enters his fighter for that last battle above Earth. As he's flying, he sees that there is an Escafil Device on his bridge (unbeknownst to him placed there by the ellimist). He does a big WTF, but forgets ingores then and starts battling. Fastforward to his desparate return to the construction site and meeting the kids. He realizes Tobias is there, remembers his vision when he was with the ellimist, remembers the mysterious morphing cube, and puts two and two together. So he sends Jake in to get it and you know the rest.