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You might want to check out the tool called ePUBPack. You then just would need to tell where your mimetype is, and it will create the ePUB for you.
Personally I prefer the Sigil editor much more than the Calibre editor, but YMMV. Although there is beauty in handcraft, that is how I started as well, the automatic creation of the opf and ncx are a very useful part of the editors. As you can open and tinker with those files as well in the editors, you can still learn a lot.
You can also use GIF, PNG and SVG. All readers *should* support that, but be aware that not all the options of SVG are supported, nor are animated GIF.
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