my @split = split(/\|/, "$html_this_file");
my $html_of_file = get $split[0];
my @prefs = split(/\#/, "$split[1]);
my $j;
for ($j = 0; $j <= $#prefs; $j++) {
    $html_of_file =~ s/$split[2]/<!--PARSE-->/s;
    $html_of_file =~ s/$split[3]/<!--PARSE-->/s;
    my @pieces = split(/<!--PARSE-->/, $html_of_file);
    $html_of_file = $pieces[1];
    $html_of_file =~ s/<script.*\/script>//gis;
    $html_of_file =~ s/<style.*\/style>//gis;
    if ($prefs[$j] eq 'a') {
        $html_of_file =~ s/<a.*\/a>//gis;
    } elsif ($prefs[$j] eq 'all') {
        $html_of_file =~ s/<.*?>//gis;
    } else {
        $html_of_file =~ s/<$prefs[$j].*?>//gis;
    }
}
[download]

Is this a typo?

my @prefs = split(/\#/, "$split[1]);
                        ^
[download]

In your loop, you are doing things that will only have an effect the first time through the loop. This may be the source of your warning (I have no idea what line matches up with the error message you got). Specifically, your substitutions, splits, etc., all act using things like @split and @pieces, which aren't really modified or differ between loops, since each loop is based off of @prefs. Sounds like you need to re-investigate your logic, or maybe just move those one-time operations outside your loop.

Thanks, I took all the pre-rendering stuff out of the loop and it seems to be working now. I had just kept adding stuff into the loop without thinking it through.

BTW that " was a typo.