Man, I really have no idea. As >>232 suggests, sometimes Apache might be setup to run .cgi files but not .pl, but if your test file is named .pl, I really have no idea what's going on. What's in the file you end up downloading if you go to wakaba.pl? If it's the Wakaba Perl source, it's an Apache issue...
Link should be obvious, no? Parent is only for admin posts. You put the number of the first post in a thread there if you want to make an admin reply in a thread.