When I download an epub from Project Gutenberg I feel the need (compulsion) to "fix" its layout and formatting. I open it in Sigil, find the files that have the first and last chapters and use Sigil's merge function to turn them into one big file. Then I select and copy everything between the start and end body tags and paste that into a new Sigil instance, replacing that empty paragraph it provides. Looking at what that produces in Sigil's preview window it's by and large readable, the main offenders being a big space between paragraphs and no indentation; since I didn't copy over the original CSS file there's no styling other than what the previewer has built in.
So I'd start with something like that; strip all class= lines and make all the tags bare. Then add some basic css file after deleting the original.
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