Slvtmong00se,
I am having the same issues. What I found was Mobipocket Creator. I import my PDF file and then edit the HTML file that is created. The output is a PRC file, which Calibre converts to EPUB really well. I have been able to "fix" some of the worst files with this process by opening the HTML file and using find/replace in notepad to get rid of hard line breaks, which are standard in PDF files. This includes creating table of contents so that I can use goto/chapter functionality.
Unfortunately, there is one set of PDF files that just won't work, even when I use this process. Since it is only 20 books of my 1400 book library, I've chosen not to sweat the small stuff.
I found this method on the Calibre threads. Unfortunately, this is a one file at a time process and can be time consuming. I am a novice at this stuff and I am still trying to figure it all out. If there is a better, more efficient way, I haven't stumbled onto it yet.
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