comment them out when I don't need them

Have you considered trying something like

warn "The code is running in debug" if $::debugging;

This way you can just say $debugging = 1; instead of changing many lines of code. vim is a great tool, but it isn't a debugger. For debugging, you need emacs. :-)

Update: You could even have $::debugging set by command-line switches, or an %ENV variable or a CGI parameter. Then you would not need to change any of the code to get some debugging info. This is great if something prevents you from touching the code, for example if it is running on a production web server.