wow, thanks a lot all for your comments. I will try them all. I am really new to all this stuff and your comments help a lot to know what to try next and that I am not alone with this manual process.
@Hitch, yes I know what you mean. Unfortunately I have tried the indd conversion to epub and given the files that I have been given, the process took me a lot more time than to copy/paste from PDF and work from there. I have seen that an indd file has to have everything in order and a very clean file so that the export work fine, even after doing the normal fine-tuning before export. So, I was dedicating more time to fine-tune everything and it was not very effective. Unfortunately for me, I cannot ask the team that creates the indd to be more cautious about this, so that is why I try to do it like this
