I’ve found what is causing most of the problems. You have Track Changes turned on for the document. There are some revision marks in the document and Aspose.Word does not support revision marks. It just treats them as normal text, therefore you see all text that was deleted and changed in previous revisions. If you can, then Accept All Changes so revision marks will be removed from the document, after that no doubling up and no deleted text will appear in the document.
Please note that left margin of some paragraphs is still wrong. This is somehow related to list formatting and I cannot resolve it now because it works fine in all my other test documents. I recommend you just reapply formatting in your original document, it should help. Just open the template document, move the left paragraph margin back and forth and save the document.