That's actually not a bad length for a lot of bird in flight shots. Which auto settings are you using? program mode or one of the semis? I get my best shots on aperture mode at between 5.6 and 8 f stops. I put the auto focus on continuous (your camera might call it something else) where it'll track motion. Then I lock on to an approaching bird that's parallel to me and pan slowly while the autofocus locks. It's also good to keep shutter speed at between 500 and 4000.