title_body: No .indd files to convert for Kindle publishing
upvoted_answer: This is going to be a challenge. There are some programs out there that do a decent job extracting text cleanly from PDF files, such as OmniPage. You might also check out pandoc, but you will have to convert the document from PDF to something else before it can help you much. You will almost certainly have to recreate a lot of the formatting, no matter what you do.
  
  It would help us give better answers if you told us what issues you have after converting from PDF to RTF and importing the RTF into InDesign.