Sacred Haven of Debauchery

The Federation really ganged up on me. The entire galaxy, except for some humans with a fleet of 2,000 against the poor bird-lizards.

Just 2,000. Well, it's not that difficult against superior forces. You destroy the defensive structures in space, and then separate the smallest and fastest ships, sending them to orbitally bombard all the enemy planets. Unless the AI has learned to divide the fleet against such situations, then yes, it will be difficult.