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i think you need to start over & check at each stage what is going on with chapters.
it will be faster if you use kindle for PC or configure calibre viewer to view mobi - then you can keep checking if chapters are still OK
this time around though I would go through each conversion screen & tick reset to default, just in case you accidentally changed something.
at the stage wherer you reckon the book as added to calibre & dedrmsed take a backup - open path - copy file. then you will not have to repeat that step.
then I guess you are editing metadata to add the picture, followed by mobi to mobi conversion to add that into the book?
check the output again there, before sending to kindle, either by viewing in calibre & checking TOC or my opening in kindle for PC
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