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I think most first try to produce a good ePUB and convert that to the Kindle format. I think you would be better of in the KDP forum for that.
There are reports I believe that .mobi files converted via Calibre are not allowed by Amazon, but I am not sure about that. Search around, there is more about that all around the forums.
Also, it is better to clean the source in an application better suited for that than in an e-Book editor. Usually that is much faster and easier. YMMV
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