Your 3 snippets can be easily converted to (far more readable) subroutines thus:

'sub {
    my( $call_ids, $call_id, $index ) = @_;
    ceil( 
        ( $call_ids->{$call_id}->{$index}->{duration_milliseconds} / 1
+000. ) / 6
    ) * 6 / 60;
}'

'sub {
    my( $call_ids, $call_id, $index ) = @_;
    if($call_ids->{$call_id}->{$index}->{ release_code } == 503 ){
        1;
    } 
    else{
        0;
    }
}'

'sub {
    my( $call_ids, $call_id, $index ) = @_;
    
    my $route      = $call_ids->{$call_id}{$index}{ route };
    my $src_state  = $call_ids->{$call_id}{$index}{ o_state }; 
    my $dest_state = $call_ids->{$call_id}{$index}{ t_state }; 
    my $juris_indicator = 'f';
    
    if( !$src_state ){
        $juris_indicator = 'c';
    }
    elsif( $src_state eq $dest_state ){
        $juris_indicator = 'a';
    }else {
        $juris_indicator = 'b';
    };
    $route =~ /^[a|b|c](1[2-9][0-9]{2}[2-9][0-9]{2})/;
    $corrected_route = $juris_indicator .  $1;
    $corrected_route = $route if $route =~ /loop|none|lnp_error|no_jur
+is_digits/;
    $corrected_route = $route if !$corrected_route;
    
    join ',', 
        $call_ids->{$call_id}{$index}{ day },
        $call_ids->{$call_id}{$index}{ day_chunk },
        $call_ids->{$call_id}{$index}{ o_trunk },
        $call_ids->{$call_id}{$index}{ t_trunk },
        $call_ids->{$call_id}{$index}{ route },
        $corrected_route;
}'
[download]

Once you have loaded them into your $agg_snippets hash, those text snippets can be replaced by instantiated subroutines in one pass using eval like this:

$agg_snippets{ $_ }{snippet} = eval $agg_snippets{ $_ }{snippet} for k
+eys %{ $agg_snippets };
[download]

Then later, when you are processing the %$call_ids hash, you can invoke them like this:

 for my $this_call_id ( sort keys %$call_ids ) {
     $count++;
     next if !$this_call_id;
     my $route_attempts = 0;
     for my $this_index ( sort keys %{ $call_ids->{ $this_call_id } } 
+) {
         $route_attempts++;
         foreach $aggregate_name ( keys %{ $agg_snippets } ){

             my $this_group_data = eval $grouping_data_eval;

             $summary_data->{$this_group_data}{$aggregate_name} = 0 if
+ !$summary_data->{$this_group_data}->{$aggregate_name};
             $summary_data->{$this_group_data}{$aggregate_name} += 
                 $agg_snippets->{$aggregate_name}{snippet}->( $call_id
+s, $this_call_id, $this_index );  
#                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                         
         }
     }
 }
[download]

That still leaves the eval of the $grouping_data_eval, which you give no information for, but it should also be possible to eliminate that eval by instantiating it into a subroutine once near the top of the code.

The overall effect should be to substantially speed up the processing. (BTW: Note how much clearer things are with: a) a little formatting; b) the omission of unnecessary punctuation; c) a little extra horizontal whitespace.)