Can you include a literal newline inside the double quotes? That would allow you to use perl -x:

<not> <gonna> <happen> : "
#!perl

.
. This is the script
.

__END__
"

.
. This is the actual file
.
[download]

So what would the script look like? How about

local $^I = '~';
local @ARGV = __FILE__;

my $seen_data;

while (<>) {
    if (!$seen_data) {
        $seen_data = $_ eq qq{__END__\n};
        next;
    }

    ... change $_ as desired ...
}
continue
{
    print;
}
[download]