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Since you ask for an alternative, here is what I do; I've edited or made thousands of epubs, then sent them to my Kobo as kepubs, and have never had a navigation error. None of this particular work process needs any coding.
Cover: I usually use Edit Metadata to put in a new cover, then use Polish to write it into the book file before editing. Sometimes, if I'm editing using the Editor and want to put in a new cover, I'll just import the file and replace the existing one, marking the new one as the cover image. (Right-click on an image file in the file browser to see many options)
Navigation: I merge and split as you describe. I often rename the files. I have never paid any attention to what the spine is doing, the Editor has always handled that correctly no matter how I rename or move them around. To make the ToC, I use the ToC Editor in the main Editor. I usually remove any entries that are present, and then use the option to build a ToC "from files". (toc.ncx is edited properly, every time) (If it is an epub3, delete the nav.xhtml and let it rebuild)
Sometimes (actually very often) I will edit or rename the ToC entries that come up from building "from files". It's really good at chapter headings if properly coded, but not so much with front matter and end matter files.
Nothing in this workflow will re-arrange your files. I've never seen any navigation error on my Kobo. I keep everything in my library as epub, and just use the Extended Touch plugin to send kepubs to the reader.
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