I have the same issues when I do similar things. Find and replace covers a lot, especially in replacing line breaks with spaces or nothing. Then I use the spell-check to more easily show me the ones where extra spaces broke up words.
Between those, then I just have to go in and hit Enter to end paragraphs wherever I want.
Unfortunately, pdfs tend to throw in strange hidden characters for their own kerning and placement use. Especially when the text is so artfully arranged around images and other decorations.
If using Acrobat, you can try right-clicking on the text you want and selecting Copy with Formatting. That gets rid of the assorted line breaks whe you paste it into Word or whatever.
Depending on the size of the file, you can also try saving/exporting it as a Word document, which will do the same thing by and large.