I went back and checked this last night and we have both sides within spec (assuming were lined up with the case) I love Wayne's book but the timing section seemed a bit overly dramatic. The factory manual was much more clear in this respect. But I know Wayne has to cater to the entire list of options that someone could be facing when building a motor.
I don't see how this could be a precision process. The book may emphasize the importance of getting the overlap "exactly" right but the bottom line is, the case seam can't be called a constant. A human being lining up a pulley to a case seam? The same exact place everytime?

Maybe I'm missing something?
You could be .010 off on either side of that mark and never detect it (you can't tell the difference). Neither can you bring the pulley back to the same exact spot at the case seam on subsequent rotations.
$.02
Ken-