I found a great little tool for reformatting TXT files many years ago called Textify. It's a freeware windows command line utility that takes a text file as input and outputs a text file reformatted to your specifications. Here's how it works:
1) When you start the program you hit C to continue.
2) It then asks for a file name (it works best if you put the files you want to work with in the same folder as the textify.exe program). Type in the filename (without the.txt extention, it adds that automatically)
3) It then asks for a description of your text file (0- Carriage return after EVERY line instead of after each paragraph; 1- Single carriage return after each paragraph; 2-Two carraige returns after each paragraph). Pick the one that describes your file.
4) Next it gives you a few paragraphs of text about strange extra spaces in some documents meant to make things appear to be justified text and asks if you want to remove them. This is almost always a good idea.
5) Finally, it asks how you want the output: 1- One carriage return after each paragraph; 2- Two carriage returns after each paragraph; 3- Output as HTML.
It's a perfect little tool for just the type of problem you're having with CRs after every line. Depending on other oddities that may be present in the translated PDF-Word-TXT file, it may or may not do a great job, but it works well for me most of the time when I run into weird TXT file line break issues.
I had a hard time finding a site to download textify.exe from, so I put a copy up on one of my own servers. You can download it directly from this link:
http://www.quorlan.com/tools/textify.exe. Hope it helps and enjoy!.
Q