You'll want to add the e modifier to the s/// function:

$input =~ s/(\.)(.)(\.)WI$/'_'.lc($2).'_w'/ge;
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(Note that you need to group and remove the periods as well in this).

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Dr. Michael K. Neylon - mneylon-pm@masemware.com || "You've left the lens cap of your mind on again, Pinky" - The Brain
It's not what you know, but knowing how to find it if you don't know that's important