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I use the Modify ePub plugin and Convert to automate many fixes. Convert will fix many things, if you add enough things in the Styling and Transform sections of Look and Feel.

Some of the things I fix automatically in most of the books I convert are (I run Modify and then Convert):

All indents are changed to 1.2em, all line-heights are changed to 1.2, remove blank line spaces (but sometimes I have to manually edit the paragraph CSS code to fix this or manually delete the lines that add the blank line spaces), change the "body" side margins to 30pt from 5pt, add the Charis font and remove all other font style CSS codes in the .css file, remove all the CSS codes that are invalid according to Calibre (these are all in the Transform section), justify all text in the paragraphs (manually have to justify some of the sections at the beginning of the books), change the CSS code for cover images that are coded as auto and auto to 100% and 100% (I have a macro that adds the CSS code for this in the .css file, so I only change the class to calibre3a and hit ctrl-shift-5 to add the CSS code quickly), paragraph font size is changed to 1em from whatever the original code is, and many more automated things I can't think of at the moment.

Convert removes all the unused CSS codes, Modify removes a lot of things that shouldn't be in the files, and on and on.

I also highlight all the files and run the ToC plugin to edit any ToCs that need to be fixed (like add ToC from files when there are no ToCs, rename chapter numbers to Chapter 1, Chapter 2, etc, rename Chapter One, etc, to Chapter 1, etc). The ToC plugin will open the next file after you click on OK for each prior file.

My only wish is that Convert would do the Check Book and Automatically fix errors automatically during the conversions. I have to do this manually, but there are usually very few errors found after I run the Modify and Convert plugins.

When I get done doing all of this (most of it is automated), my files are very clean looking and they all have the same format in the text for the paragraphs. I'll manually edit the CSS codes for some of the beginning pages, if there is too much top and bottom space or when I notice other things that should be fixed.

Some files are so badly coded and have tons of <spans> and other poor coding that it can take much longer than five minutes to edit the file properly. If I really want a certain book, I will spend the time to edit everything, including the spellcheck and the Report (to fix punctuation and remove improper symbols due to scanning errors, etc).

I also have edited hundreds of Open Library books to fix everything and format the files properly, in addition to modifying and converting many thousands of ePub files.