Coming dead on at me is the hardest shot for me to make...I am using a D7000 which has all the bells and whistles I need to make the shots. I am using a single point focusing method and autofocus mode generally shooting in the ISO 200 range, 1/1250 at f/4 or 5.6. If it is a static shot, I will drop the shutter speed and go for a greater DoF but generally not higher than 8.
Any suggestions other than continuing to practice?
Birds in flight is definitely one of the more challenging areas in photography - demanding of both photographer and equipment.
I like to have my shutter speed at least 1/1000 second, and am usually shooting wide open, or stopping down a full stop if there's adequate light. So you seem to be on pretty much the same track there.
Regarding AutoFocus, different cameras offer various options to "fine-tune" performance. I use Canon, and am not familiar with Nikon's system, so can't give specific recommendations. But I'll describe how I customize my settings, and you can see which of these, if any, is applicable to your gear.
I also use a single manually selected focus point (typically the center point, but sometimes moving left or right, depending on the size of the bird, the direction it's flying, and how I want to compose the picture). Custom Function settings for my camera provide an option to "auto-expand" to the set of nearest Focus Points if the tracking system needs to, to kind of "hand-off" the focusing if it gets out of the range of the selected Focus Point.
There is also a sensitivity control, which actually works a little counter-intuitively. This is set on the slower end of the scale: what this does is cause it to delay trying to completely refocus if it loses the original focus point. So, for example, if something comes between you and your subject, it won't immediately try to refocus on it, but will delay this, and theoretically maintain focus on your original subject.
There's also a setting to determine whether or not the camera will go through its whole focus range in order to regain focus of the subject, when it is lost. The idea here is that by setting this to "off", you won't lose valuable seconds trying to regain focus by having the camera look through the entire range of focus. Sometimes this helps, sometimes it doesn't.
Also, many times the lens will allow you to set a focus range - sort of a near, medium, and far, to accomplish the same thing. If I know my subject won't be coming too close, I'll select the 'far' setting, so it can narrow its attempts to lock and regain focus.
And I assume you have the camera in what Canon calls "AI Servo" where the AutoFocus system is continually working and maintaining focus (as opposed to the "one shot" where it achieves focus, and then locks this in). Also, I have found it helpful to choose Canon's option to have AutoFocus controlled by a button other than the shutter button, thus fully separating the act of focusing, and the act of triggering the shutter. I use the * button on the back of the camera with my thumb. As long as I have it pressed, the AutoFocus is engaged in a continual mode. If I remove my thumb, it stops refocusing, and the previously selected focus is locked in. Give me both AI Servo and One Shot capability, without having to change any setting. I have no idea if Nikon provides this as an option, but thought I'd throw that in just in case it does.
Hope this helps, and doesn't confuse!