[sourcejedi]

I would strongly recommend looking for an alternative to Calibre for ebook creation. Although I strongly doubt you can get much smaller files, unless you're doing something really weird.

In my opinion / limited experience, Calibre was created for the purpose of converting & syncing ebooks with a personal e-reader. I would look at special purpose software like Sigil instead.

Search for "epubcheck" and "epub preflight" if you haven't seen them already.

I dunno much about PDF. You should make sure you know exactly what you want of it. Here are some possible questions to think about - do you want people to be able to print it? Or does it need to be readable on a 5" e-reader without reflowing? Do you want reflowing to work?

Spoiler:

I observed that Calibre will convert HTML files with no explicit alignment to EPUB files with a specific alignment (e.g. fully justified). That gives users more control, because many e-book readers don't have an alignment setting. But if your e-reader is like mine and *does* have an alignment setting, Calibre's formatting may effectively disable it.

I think it also does explicit paragraph formatting, i.e. applying either a first-line indent or a blank line between paragraphs (and this has the same effect re. user control and e-reader settings). I believe it even sets page margins (!).

I also observed that it's happy to convert HTML to EPUB, and explicitly mark it as being of language "UND" (undefined), without prompting the user. Again, this won't affect most e-readers, but if your e-reader knows how to do automatic hyphenation (which makes full justification work a lot better), then it needs to know what the language is.