Run IIS web site with 'System account' isn't a good pratice, I strong recomend you to run your script with IUSR_<hostname>, as like default, and set the correct permission on the files that you need.

But if you really need a power user to run your script, you can change who is running your web application by 'Directory Security' tab of your web application configuration property, following :
* Click 'Edit' botton on 'Anonymous access and authentication control';
* On 'Anonymous access', configure the user that you want, like administrator, and go selecting 'Ok' botton on all windows.

Last advice, do not do it, especially for a public web site. For your question, I think you don't have a good skill on Windows enviromment, and maybe didn't take care of all configuration for a 'security' IIS server.

Try do run your CGI with a less security as a possible.