AF was set to AF-C, release priority, 9-point dynamic-area with the center point selected. Custom setting a3 (focus tracking with lock on) was set to Normal.
I'm not sure what you mean by an "af-on workaround."
The 6 fps bursts were plenty for what I was shooting. I really don't rely on the burst mode to catch a fast-action moment. Even the 9 fps of the D3 won't guarantee ball-on-bat.
Yes, I was shooting the 120-300 handheld. Not something I recommend; the 120-300 is a heavy lens. (My monopod was occupied by the D3 and 400 f/2.8, otherwise I would have used that.) AF of the 120-300 isn't as smooth as that of the 70-200, but it's accurate and works well. Yes, it does feel a little funny to have such a small body on the end of a big lens.