To pull ISBN ... use the template elements. There are three that are relevant. Likely the third is most useful ...
[OL_ID_ISBN10] ISBN 10 digit
[OL_ID_ISBN13] ISBN 13 digit
[OL_ISBN] 13 digit ISBN if available, else 10 digit ISBN, else blank
Please review this reference ....
https://code.google.com/p/openbook4wordpress/wiki/templateelements
Re: "code left behind". OpenBook works like any editor toolbar. If you use the "Bold" feature on a toolbar, it adds <strong></strong> tags that do no disappear when you remove the toolbar. OpenBook also writes HTML (if you use the default option) or a "shortcode" (if you use that option). You can edit or remove the results as you like.
The default formatting was selected based on user feedback during the development phase. But you are completely free to format things any way you like using the templates.
You seem dissatisfied. Ok. Note that the plugin was an independent development project by me, not a project of the Open Library team (who are wonderful).
Cheers, John