I followed the suggestion and placed the output in
https://gist.github.com/2930025
What the program does:
calculates the distance from the center of the text for the stroke
number to the start point of the corresponding stroke. If the distance
is greater 15, the text is considered "far from stroke". The stroke is
reported, if there is another text that has a distance<15 to the
stroke start, and this other text is "far" from its own stroke. The
found stroke is most likely involved in a mixed up stroke numbering.
My guess is that this is a relatively conservative way of reporting
that underestimates the number of actual bugs in the files. For kanji
with many crowded strokes there is probably no automatic way of
detecting bugs.
The program (in C#) is too hacky to show to the public and I don't
feel like cleaning it up. Sorry, I will keep it private.
Greetings, Jan