The <p> alone is not a bad thing....
MobiPerl code strips all ending </p>'s when converting from .mobi to .html. I see the same thing when my Mobi2IMP program converts .mobi/.prc to .imp as the intermediary .html is left exploded with images.
For example, here is just the .html file (without images) extracted from my Moonport.prc and notice that it is ONE .html as well!!!
I know calibre adds </p> to .html files that get converted to .epub so as to comply with XHTML 1.1 Strict (every tag needs a terrminator tag). So perhaps feed it to calibre and take the resulting (x)html. You can even tell calibre to not-split the files based on page-breaks and/or 300K chunk size!
Can you give a sample of that BAD code?
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