To be honest, I am a newbie in bird photography. My approach is try and error. I did fail a lot *films* at the first try, but I also learned a lot from mistakes. Those of u really want to know how to shoot birds, dont rely on my post, better read something professional, hehe... But we can communicate directly here, that's the advantage!
Ok, I found manual focusing works difficult for me. You know someone has pointed out that for bird photography, anything (i.e. lens) shorter than 600mm will be useless. It's true but as we are talking about birds in the JBP, so this is quite another story. I use 70-200mm with a 1.4x TC. The D60 itself has a 1.6x multiplier, so all in all about 450mm max. Birds are generally not really far away, wihtin from 20m - 100m. And with D60's 6MP, i have quite big room to crop later. But anyway, for a decent bird photo, dont make the bird look too small.
I dont use manual focus coz feel that I cannot react fast enough to the change of subject's distance. In the best situation, birds fly from left to right or reverse, so the distance is almost not changed. In this case manual focusing is ok when panning. But you cannot predict how birds fly in most cases. In order not to loose many opportunities, I use AI focusing, so called continuous focosing. The drawback of AI focusing is that you have to put the bird on one of the focusing points (usually central point). And another drawback is I cannot focus on the bird's eyes but body instead. Otherwise the focusing point may hit the background and bounce back and forth.
I have learned to follow the golden rule: if you see it, you have missed it! in sports photography. It's true that if u see the most beautiful moment, you actually have missed the opportunity to capture it. What I follow is to predict the bird's action. The hit rate is dependent on experience and luck. So far I dont feel good enough in this aspect.
I use handheld coz it's not flexible to use tripod. As I put it b4, I use shutter speed prority 1/1000s, so hand shake has already been reduced. But when bird fly fast I do get blur image. Once again, need experience and luck here.
IMO, auto focusing system can react fast enough if you always point your camera to the subject correctly. What may fail you is not the camera, but the cameraman. Many times I react or shake too much, or dont fire in time. Solution: go back and practice