Hello Roger,
Thanks for popping into the forum with your questions, they tend to be quite a bit easier to answer on a keyboard.
You are correct, the A side and B side of each board are stuffed quite differently, but the A side and B side between the pair of boards will be the same.
The first step of installing the LM431 is on page 16, and the second on page 17. It may seem a bit odd that both sides of the board get the LM431 regulator considering the differences in parts population, but this is indeed correct.
As far as what goes where, using the photos in the manual is the most helpful way of ensuring that everything is in its place. If you find any steps in the manual for assembling the PCB that do not call out A side vs. B side, please let us know and we will author corrections.
Sincerely,
PB