I gave up using CGI.pm years ago when I went to mod_perl and never looked back. I use $r->args() or Apache::Request. I don't think the performance difference you describe is enough to merit choosing one way of reading args over the other. Pick whichever one is easier to read for you. Either way, I think CGI.pm will give you an array ref if you send in identically named args.

Are you using Apache::DBI? That would explain why you have connections open to MySQL.

As for the timing, it's hard to say based on the code you've shown. It's possible that some processes are failing to get database connections, or your machine is swapping, or any number of other things. Your plan to take things out until it stops and then slowly add them back in is a good idea. That always works for me.