Are you sure about VR? I always had it on when I used the D40.
Interesting. Not sure what to make of that, then.
Autofocus was on AF-A so I will switch to AF-C and see if that helps.
Always use AF-C for panning and any subject that's moving, for that matter. AF-A attempts to detect whether you want single or continuous focusing, there's no sense in adding that guess-work when you know what you need.
As for the Focus, is the 3D tracking the best option?
Now, that one's tricky. It depends on a number of environmental variables.
From what I understand, 3D tracking attempts to follow the subject around by learning its physical characteristics (mostly colour and contrast, I think, so, obviously, it works best when your subject contrasts with the background) of whatever you place under the AF sensor you've manually selected, and then will automatically select whichever AF sensor falls on top of the subject as it moves around the frame. When it works well, the idea is that this lets you concentrate more on your composition and allows you to change your framing without having to manually move the AF sensor around. The D90 has a limited implementation of this system compared higher-end models (ie.: D300, D3, D7000, etc.), naturally because it has fewer AF points.
It takes some experimenting to figure out how this system will work best for you. In some cases, it probably just makes more sense to know your subject, predict its movement and plan out your composition before-hand to be able to select the correct AF sensor.
