Indeed, dropping the "\r" from the traditional Win32 line ending of "\r\n" means that Notepad.exe (and others of the more stupid Win32 programs) don't recognize the bare "\n" as a real line ending. So you get all of the code run together in one big line that looks quite like an unintelligible mess.
My first suggestion would be to get a better editor. But restoring the line endings to "\r\n" is pretty easy. If you have (a native) Perl on Win32, then you can do that as simply as:
perl -pi-i -e "BEGIN{@ARGV=map{glob}@ARGV}" *.pl
REM check the new *.pl file contents
REM if everything looks good, then:
del *.pl-i
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