Right now you're pulling the entire file into a scalar while removing the junk and then lowercasing the words, and then counting them. Do this instead, just pseudo code since I can't really read your regexs:

while(<STDIN>) { 
    s/remove junk strings//og; 
    my @words = split(/\s+/, $_); # split into words 
    foreach my $w (@words) { 
        $MyWordCount{lc($w)}++;
    }
}
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I would imagine that is faster than what you are currently doing. I say this because this way you aren't having to accumulate everything into one big scalar.