I also had the ligature problem with a PDF file. My eventual solution was to open the file in Foxit reader - which replaced the ligatures with separate characters. (I also tried this with Adobe Reader, but the result was less than successful, with odd blanks sprinkled at random through the text - Foxit works better, and it's free.
http://www.foxitsoftware.com/products/reader/ to download it.)
I then selected the entire text using the Text Selection tool (requires some careful manipulation) and copied it to the clipboard. I then opened Word and pasted the clipboard into a new file, then turned on the "Show/Hide paragraph marks".
This approach made every display line end with a paragraph mark, which was not the desired result. So I did a search-and-replace to replace all periods followed by a paragraph (.^p) with a vertical pipe (|), and all closing quotes followed by a paragraph (”^p) with a vertical pipe. These marked about 98% of the "normal" paragraph breaks.
I then removed all paragraph marks and replaced them with a single space. Finally, I replaced the pipe character (|) with two paragraph marks (^p^p) to restore the appearance of normal paragraphs.
A quick search of text will allow you to find chapter headers (or other similar text) and make them into Word header styles - this is not absolutely necessary, but makes things more tidy. Then you can save the file as RTF and import it to Calibre for conversion to other formats, if desired.
The resulting text was 98% perfect. There were a couple of occasions where a paragraph was inserted incorrectly, but this was a vast improvement over the previous text with all of the ligatures screwed up.
I haven't tested this approach with other editors like Google Docs or Open Office, but it should work, as long as they allow you to do a search-and-replace for paragraph marks.
Total conversion time from PDF to RTF was probably about 10 to 15 minutes. If I were doing this on a regular basis, I would probably record the search-and-replace procedure to a Word Macro, which would make it even faster.