Fast Action Focus technique help needed

I need some advice on getting quick moving small mammals in focus. I suspect its part poor practice on panning, but I think I may be using the focus activation unwisely as well. When the subject is standing still or slowly walking, my D300, 500 f4 + 1.7 TC set up works great.

I spent an afternoon with the Pikas in Rocky Mountain National Park, lined up so they were running almost directly at me with grass in their mouth. If you've spent any time with Pika's you know they can go about 25 mph in a blink of an eye. The shot I really want is a pika coming right at the camera with a mouth full of grass, stopped in midair, feet out front like super pika.

My settings on the D300 were, Autofocus activation with AF button, also tried with Shutter AF activation, I tried 9 and 21 point dynamic, 11 AF points, Continuous focus mode, release and focus, Focus tracking long. All my results were the same, I have blurred pikas and sharp rocks. I know shutter speed plays a big role, but the focus location was always behind the pika's head where I tried to keep the focus point.

Setting on the 500 f4 was AF/M and full range on the focus limiter.

I would follow the pika for about 3 to 10 seconds while it made its run.

The techniques I tried:

1. I would start the AF as soon as they started running with the AF activation button.
2. I tried hitting the AF activation button multiple times, harder to track the pikas
3. I tried with the Shutter activation as they moved
4. Lastly tried the shutter tapping it multiple times during the run, really hard and caused some vibration, beyond the focusing problem.

So from what I learned, continuous autofocus does not equate to 3 to 5 seconds of continuous panning. Does that sound right? Should I narrow the time I follow the subject in action and take just one burst instead of doing it multiple times? Lastly 70% of the time the selected AF point was right on the Pika, not behind in the rocks.

So I seek the sage like advise that is here. What should I be doing, or trying to do?

Have you tried MF? No kidding, especially if you have control of the Pikas, telling them where to go. That's what people used to do. Pre-focus at a certain point (so much the better if you can set up a reference point). Press the shutter right before the Pikas reach that point. If the timing is right, you get the picture. You don't even have to look into the viewfinder (use a tripod). And that's what people used to do, too, because if you can see it in the viewfinder, it's too late already.

Jared in that situation I would set the Dynamic AF area to nine points and the Focus Tracking with Lock On to Short Would probably not use Dynamic.

For acquisition try to prefocus on a area short of the intended exposure point. Do not activate the AF but let the target start to come into focus then activated and make your exposure. I have used the back button for activating the AF but it is not a causal thing your doing. I find it takes time to get used to the change and going back from front to back is not a good idea. I used it for six months and I'm back to using the conventional way.