@JSWolf - I follow the same approach as the calibre conversion logic does of putting the replacement cover image and html page in the root of the epub, rather than trying to "guess" what the image and content directories are named. It is a possible enhancement to try to put them in similar places that I could attempt, though it is a pretty low priority given most users don't care about how the epub is structured internally (since the likes of Sigil will reorganise the content anyway).
As for the NCX - I need you to PM me a link to the epub in its "before" state so that I can see for myself what is happening. Certainly there is code in there intended to re-point the ncx to the new cover, but obviously you found a situation which beats that logic which is most definitely of interest to me.
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