CGI.pm has a debug mode, which you can use to run your program from the command line, and pass your CGI parameters as key/value pairs.
It has another feature that you can use to save your params to a file, and then read that file back in later.
What I've done is added the code to save the params to a file, and run my program, via a browser. This also facilitates my abilty to insure that the browser is sending the correct data.
Then I change the code to read the params from the file, and run it as often as I need until I have everything else debugged.
Once you've got the program running to your satisfaction from the command line, you can run it via nytprof to figure out what is taking all the time.