I extract PDFs to Word docs (or RTF; the file is the same from my viewpoint), and then edit the Word doc. If I were more fluent in HTML, I'd extract to that--and expect spend the same amount of time editing the HTML file as I spend on the average PDF-to-Word conversion.
I generally have to fix the page sizes & margins, remove text boxes, change pictures to inline with text, and do odd things to get rid of the page numbers & headers. Then I fix the paragraph settings starting by making them all single-spaced, and removing the right & left margin indents if any; if it's reasonable, I change them all to the same before & after amounts and justification. Then I set the font--make it all one font, use find & replace to fix the sizes, make sure it's all 100% size, not condensed or expanded.
I'd expect HTML files to work better if the fonts were normalized, remove the extra "div" sections and "align" tags, get rid of tables that force the page structure.
Basic novels should transfer nicely. Of course, basic novels probably transfer fine from the original PDF straight to Mobi. It's when there are other formatting aspects that the conversion breaks down, and none of the auto-converters shines as the best one, because PDF wasn't designed to be a convert-from format.