As you say yourself, they should work. However there is nothing stopping you from using mod_perl while still using your scripts as plain CGI scripts. You then have time to test each script running under mod_perl and CGI to see if there are any regressions. Even using strict it is my observation that some variables are not always reset when the script is continually running, and thus you should either change your script or use Apache::PerlRun instead.
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