And the Replacement Parts Manual wording should be flush with the red header line and the Card Dispenser... Header is an H1 and should be at far left column not with that dotted line going vertical down the page. Not sure if I hit something and can't revert to or remove setting.
It looks like your pgf format is set to respect Side Heads. Open the pgf designer and try setting it like this...

I have no idea why the script would have changed your pgf formats. The depends entirely on how the script was implemented -- what the authore makes the script actually do.
I suspect you could import formats from a document where you did NOT run the script, and it would return the formatting to the way you want it. I hope you back up your work!