In addition to the excellent advice you've already got from McDarren it's worth pointing out that CGI::Carp is a very useful module for getting nicely formatted error messages out of a CGI program. In particular, I recommend the "carpout" function which allows you to set up an alternative log file that CGI::Carp messages get written to.

You should also be aware that a CGI program really isn't that much different to any other Perl program and you don't need to run it on a web server. As long as the required inputs are set up, you can run a CGI program from the command line. I've debugged many a problematic CGI program using Perl's built-in debugger.