For shooting birds I usually use 9 or 21 focus points rather than all 51. Try to keep the subject as close to the center of the frame as possible.
If you find that focus jumps off of the subject often then try setting Custom Setting A3: Focus Tracking with Lock-On to a higher number. You may have to experiment with this setting to find what works best for you.
I do not recommend Auto Area AF or 3D tracking for birds and aircraft. Auto Area takes away all of your control of the AF system and the 3D tracking option works best with people and closer subjects.