Hello Maddambutterfly hope your book is a success I know how frustrating self publishing can get but what a sensation when your mind's work is available for all eyes & your wish has finally become true.
I create my books in Microsoft office word, never had problems uploading to Kindle saving my file as 'Microsoft 97-2003 document otherwise Amazon won't accept it.
I don't know if any of the above helps, the formatting seems impossible at first but really, I have been there, quite easy once you gone through the practice a few times.
It is difficult to explain me writing like this so you may have to do a little more reading but the concepts are super learn able and 'smashwords dot com' have a great free info book especially for new authors to publish work on a wide range of digital book selling platforms, it can be download free titled 'smashword style guide' showing you the correct way to format your 'book/novel' documents which usually Kindle accepts.
Hope this helps you, well done for your hard work, looking forward to seeing details of your book on the world wide web.