>does that guide cover all of the config stuff?
If there's anything else required beyond what I wrote on that page, then I don't remember it off the top of my head

One thing is to always remember to restart Apache after you've changed anything in the config file(s), otherwise your changes won't be live

If you're still having issues, I think you should first try installing a very simple CGI/Perl script just to check it's all actually working (if you haven't already) - the more complicated scripts with lots of moving parts often come with their own issues, or are just more difficult to configure

>if a file is UNIX LF then it doesnt need dos2unix right?
Correct - conversion is not necessary if it's already Unix-type to begin with!