Some code might clarify. The man page to read first is perlsec. Tainting and setuid are very complex issues. Here's a transcript of what I think you were trying to do originally. Note that the last prompt "$" is run as myself instead of root.

# cat s.c
main(int ac, char **av) { execv("/home/thayer/foo.pl", av); }
# gcc s.c -o s
# chown root s; chmod a+rx,u+s s ; ls -l s
-rwsrwxr-x   1 root     users       11394 Dec 15 11:43 s
# cat foo.pl
#!/usr/local/bin/perl -T
print "$< $>\n";
# ls -l foo.pl
-r-xr-xr-x   1 thayer   users          43 Dec 15 11:42 foo.pl
$ ./s
3068 0
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When it comes to suid and perl, running on the command line is different than running from a real file. In unix there's a race condition running scripts, #! files, between the time the kernel detects what script program to use and when the script actually reads the file. Using a compiled wrapper or sudo are common work-arounds.