I would like to take an annotated pgn file, and convert it into an ebook I could conveniently read on amazon kindle (or its pc version), or android/Ios device. It might have to create diagrams where needed and make the book easy to go through without an extra chessboard. It would be good if the output format allowed to upload it to amazon store as well. Does such software/tool exist?
This may or may not be your cup of tea, but if you are a LaTeX user, then SCID's LaTeX export feature produces ready-to-compile LaTeX source that yields rather nice (IMO) PDFs quickly and painlessly. There are a few options regarding how/whether comments and variations are to be displayed, and diagrams are automatically included wherever you have inserted a diagram NAG
D into the game score (which can be inserted the same way that move annotations like
!? are when using SCID). Here's a cropped screen grab from the PDF output of a fake sample game: