What I do is remove headers and footers and convert my pdfs with Calibre. The resulting txt or rtf usually contains a lot of residual formatting. To get rid of this I use the automated editing tools in
Machine Age Reader to remove things like extra lines and spaces and to connect broken lines and paragraphs. When I get it as clean as I can with the auto tools I proof the text (still using Machine Age Reader) and fix any remaining problems manually. In case you can't tell, I really love this program. The tools are perfect for this kind of work. It has saved me many miserable hours manually removing line breaks and extra lines. I also like the fact that it lets me edit while displaying the text in proper, 2 page, computer ebook format. Reading in notepad always gave me a headache.
I'll try running your file through Calibre and Machine Age Reader tomorrow. I'll let you know how long and how many steps it takes.