Here's a guess what might work: Put all the .pl files in /cgi-bin/, and make a separate directory for the rest. Then edit wakaba.pl, and after the BEGIN statements at the top of wakaba.pl, put in something like:

chdir "../imgboard";

That is, the relative path to the board that holds the files on the server.

Then, change this line in expand_filename():

my ($self_path)=$ENV{SCRIPT_NAME}=~m!^(.*/)[^/]+$!;

to something like:

my $self_path="/imgboard/";

Or whatever the path to the directory is, as seen from the web.

Finally, change all the lines like this:

make_http_forward(HTML_SELF,ALTERNATE_REDIRECT);

Into this:

make_http_forward(expand_filename(HTML_SELF),ALTERNATE_REDIRECT);