as i can understand your question their are four ways to edit the mobi file the way you like:
1- if you have the original files that you used to create the mobi you can use them again to create the epub as for example if you have word files you can open them and then save as html filtered then edit with sigil or any html editor the way you like then save as epub which is directely in sigil or use the edited html and build the book using sigil to epub.
2- the converted files in calibre (try converting again of mobi to epub after downloading lastest made calibre) which after conversion are epub then save to disk in calibre could be edited in sigil or use calibre to explode epub then edit the html or xhtml in any html editor or just name the extension of file which is epub to zip then unzip then edit internal html then zip again then rename again to epub and use epub viewer to see the results.
3- install active perl or activeperl then drop the mobi file over mobi2html.exe the file will be exploded and edit the html file then save your newly edited epub.
4- install active python then use the script called mobiunpack.pyw to convert the mobi file to html then use script MobiML2HTML.pyw to convert the html to xhtml then edit the resulting file with sigil then save to epub with sigil.
you may need when editing with sigil to may be decrease the size of images in the resulting folder which accompanies html from previous solutions to may be roughly 300*300 or so then delete the pictures in epub from both within the text of ebook and the images folder in book view in sigil then add them again with the previous resolutions making sure that they are inline with the text at the desired spot of text that you need to insert images where you press by mouse cursor in the desired spot then use the option insert\image in sigil and see the results if fine
you may also need to use the chapter break in sigil to break the xhtml file to several chapters (you use that between end of every chapter and beginning of the next chapter)
last you may need to define the heading of chapters as heading 1 or 2 or 3 etc in sigil then use tools\toc editor to make sure the toc made the right way and all toc entries are correct then save the epub and test it first by adobe digital editions or your nook device.
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