Congrats on the new lens. I would recommend going with a full gimbal head (Wimberley, Jobu, to name two) for the 400/2.8. The gimbal will give you a range of motion that you would not have with a standard ballhead. When properly balanced the camera/lens combo will handle easily and up, down, left, right motion will be smooth. It would also be easier to mount the lens since the clamp is in the horizontal position and you would place the weight of the lens on the clamp and tighten.
Another option albeit less optimal, would be to use a ballhead like a Markins Q20, RRS BH55 or Arca Swiss Z1 and a Wimberley sidekick. This would give you two heads; a standard ball head for smaller lenses and a side mount gimbal for the 400/2.8. A potential issue would be trying to mount the lens on the sidekick since you would have to use one hand to balance the lens into the clamp on the sidekick while using the other to tighten the clamp.
Another consideration is how you plan on carrying the setup when in the field. If you are considering carrying the setup over your shoulder then a full gimbal is the head of choice since it is designed for that type of stress. Doing the same with a ball head and sidekick would put extreme stress on the ballhead’s panning base, which is not designed to handle that amount of stress.
Several here use a Series 3 tripod for big glass. The main reason is that a series three is the best compromise between stability and portability. I assume your lens is the VR version and VR would help minimize vibration that you may experience on the series 3. To get the most from that lens would require a series 5. However, the size and weight may be prohibitive depending on how you will be using it.
I have a series 3 (3541LS) and a series 5 (5542LS) that I use with my D300 and 500/4 AF-S non-VR version. I find that the 3541 works ok but the 5542 works great when it comes to stabilizing that lens. Your 400/2.8 is heavier than my 500/4 but VR is the great equalizer.
I have done tap tests with the D300 and 500/4 mounted on a Jobu Pro full gimbal mounted on the 3541 and 5542. On the 3 series after tapping the lens it takes approximately 3-4 seconds for the lens to settle. On the 5 series it take approximately 1 second. The difference is significant but as I mentioned if your lens has VR it is the great equalizer when it comes to vibration.
So to summarize if you have VR a series three will be adequate but a series 5 will be better. A full gimbal will be preferable over a ball head and sidekick or ball head alone.
Hope this helps and again congrats on the new lens.