I checked the box to have each new post start on a new page, but it didn’t do that.
Would you mind sharing the URL of your site where you’re using Print My Blog? Then I could see what’s going wrong. There’s likely there’s some CSS code from your theme that’s preventing the pagebreaks from being added.
Is it possible to remove part of the text before saving the PDF?
Kinda. You can add the CSS class “pmb-screen-only” onto the paragraphs and content you want to not appear in PMB printouts, and then they’ll disappear from printouts. There’s a FAQ about this.
Can I remove the comment box at the bottom?
I’m not quite sure what comment box you mean. Having the URL of your site (or at least a screenshot) will help. Maybe you’ve selected PMB to show comments on posts? If so, you can just uncheck it on the print setup page (screenshot).
Does that all make sense?