I can hear this cut

One question, what are the standards to accredit an Animation Director?
For example, in this sequence, according to the book Groundwork of Evangelion The Movie 1, Takeshi Honda redrawn each of the frames of Eva 02 in cuts 10 and 11

It depends on the case most of the time. If the AD redraws the artwork it isn't tagged. Most anime (especially modern titles) see lots of AD work between an animators layout/genga and what appears on the screen, so it'd be a bit of a mess to keep track of, especially without specifics. However, if the AD has great influence on the cut and adjusts the movement and timing (or the layout is rough enough that it can be said the AD brought it from the ground up) there's a case for tagging. The same can be said for when they redraw a cut completely. Not sure if I could say Honda is worth tagging here without seeing the before and after... but Muraki is a pretty prolific animator so I doubt Honda did much for it besides art adjustments.