OK I must have been seeing a cache of book as the next day all of the alignment issues were resolved by using the moodle default theme. I went into one of my non production moodles, added the same custom theme and book then set to work. Obviously the issue was theme related and book/styles.php was fine.
I went into the custom theme and found theme/companytheme/styles_layout.css which was naturally set to override moodle's default style sheet. I scrolled down to modules, looked at the way each one started and terminated, then just copied and pasted the content of book/styles.php after the last mod listed.
After that was done I added a READMESITEFIXES.txt to the site so that future hires will have a clue and maybe even put thier own notes in. Anyway I am documenting it here for others too.
YMV, never try this on a production moodle.