+1 for Diaps plugin
I would cleanup as much code as I could while the books were separate .
I have been replacing the pair
deNaked <spans>, but use care with <div> that might be confining a 'Block'
<span class="only italic attribute class"> with <i>

It would not hurt to ADD you standard (FULL set) stylesheet and shift over to it as you go.
Once you have run EPUB MERGE, Simply S&R the redundant sheet names to a single name (IRRC Epub merge adds adigit to the name if it finds a tie)