The question is a bit confusing...you ask for a union, but you code snippet looks like you're looking for the intersection. Union first. For small hashes this is really quick:

%union = (%first, %second);
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For large:

while (($k,$v) = each %first) { $union{$k} = $v; }
while (($k,$v) = each %second) { $union{$k} = $v; }
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(makes sense once you consider the memory usage for the first snippet.

For intersection, all you really need to do is change $matchWords to $matchWords{$k}++ the iterate of then matchWords looking for values == 2