Haven't worked on CGI/perl for a while, recently I am reworking on my perl scripts for star5.ca website. The following items should be checked when you got the 'Internal Server Error" in Perl. GoDaddy has no server log enabled by default, so you have to be very careful in doing CGI/Perl programming.
1. File permission (your perl program should have 755 mode)
2. DOS ending (your perl program should be using unix line ending, instead of dos line ending. A lot system will complain of "file not found", because of the ending issue)
3. Path to perl (usual !/usr/bin/perl)
4. Library path (use "path to your local library"), to support local perl modules.