Although you’ve found out the PDF file, converted to ebook EPUB or MOBI will retain the text (well most of it), you’ve also found most of the formatting has been lost. PDF is a dreadful format for ebooks. I don’t see an easy way round the problem unless you have the original unprotected PDF file. You are going to have to do a lot of reformatting.
There is no way of telling if you’ve done it wrong the first time as you haven’t saved any version of it. The only way round is to do an extensive copy and paste job, but this will be a pain in the backside. There is a good blog post on how to get around PDF without using a computer called How to convert an Adobe PDF document to a digital one. That is great for doing a quick edit, but I have found that the conversions are not necessarily the best they can be. It is also worth adding that PDF has its own set of problems and problems in PDF are not just that the conversion isn't perfect. What it means is that the conversion will have a few flaws in it and those flaws will make a PDF read out of line, hard to read and have a.