Most PDFs have alternating headers on every page. It used to be fairly easy to remove them in Calibre, but Calibre has changed/upgraded a lot since I fixed all of my PDFs a few years ago. The search and replace functions are different. Still the same principle, but the instructions I used from Dear Author are now out of date.
I have broken apart most of my bundles. Thought about doing so with a few of the anthologies I have where I only really want one of the stories, but then I look at my TBR pile and think my time is better spent reading