I'm not sure this is the help you need. But with that caveat, I'm diving in...

You don't show an example of your output, nor of the data structures (try Data::Dumper).

For a more mundane Perl question, you have:

for my $k (sort @hash_array_keys)
{
    print FILEHANDLE $k, $params{$k};
}
[download]

which would print like so:

key1value1
key2value2
key3value3
[download]

To fix that -- adding a pipe separator -- try this:

for my $k (sort @hash_array_keys) 
{
    print FILEHANDLE "$k|$params{$k}";
}
[download]

And it seems you are working too hard to get the keys and values -- try this:

my %params = $q->Var;
for my $k (sort keys %params)
{
    print FILEHANDLE "$k|$params{$k}";
}
[download]