i had a similar problem once.
All's i did was create an i-bay (couldnt get cgi scripts to execute from the primary i-bay), and allow php,cgi,perl script execution.
Then all i did was the obvious, placed my perl and cgi scripts in the cgi folder (under the newly created i-bay), and tested them by going to the following address,
http://example-domain.com/i-bay-name/cgi-bin/name-of-script.cgi (or perl)
It is important to check the permissions required for your specific script and change them accordingly.
I usually just transfer all files to sme-server via my local network, as i have set my server to be the domain controller for my network in the server-manager panel!
Try that out!
I know it seems to be the most obvious thing to do but it worked for me!
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