in reply to
Pattern matching across two files, Need something better than grep -f!
Sorry, but I'm afraid that I'm not understanding the problem here. Just to suggest that you choose carefully your variable names:
if($split eq $split1 && $split eq $split1)
Lines like this are artificially hard to read. Is really easy to miss the "one" before the "[". You'll realize also that to name a new variable with the same name of a common function was not so great idea when you'll need to debug or expand your code some months later.