The first job when optimizing is to find out what takes the most time. I highly recommend Devel::NYTProf, it looks like Devel::NYTProf::Apache is taylored for your use case.
One difference is that you use different SELECT queries in PHP and in Perl, and never retrieve any values. It could be that PHP simply doesn't execute the query before you try to fetch a result, so to make the comparison useful, run the same query in both scripts and also retrieve the result.
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