Thanks for trying to help. I did try the epub>epub conversion with zero margins with no luck.
I've fixed the problem. What I ended up doing was using Sigil to change the CSS on the ebooks one at a time. However, since most of the ebooks had come from the same source, most had the same CSS, so I was able to correct the CSS once and then use find and replace feature to correct the rest of the books. I still had to do it to each file individually, but I didn't have to correct the CSS myself every time.