I've not used 3D on the D5 yet... Never liked it before, but with the separate processor now it is probably better. I should probably give it a fair try... I imagine it will be very situational where it works well (color/contrast/speed/etc).
My general rule is to use as few AF points as possible... which means the easier the subject, the fewer I use. I've even used auto for very fast subjects (swifts) against a clear sky.
I don't tend to use group AF, because in a dynamic tracking mode the "single point" is actually in "group mode" anyway.
I've used the 1.4,1.7, and 2x (more typically)... no issues with any of them. But it's more of a Lens/TC/Body combination thing, that will never change.
Neil, going to check the other post now.