Thank you. With a few tweaks to deal with stuff not mentioned in the question, this is my addaption of your code:

our $INT //= 4;

my %hash;
push @{ $hash{ calcScore( $_ ) } }, $_ while <>;

my @grpKeys = sort{ $a <=> $b } keys %hash;

my @oldGrp;
while( my $next = shift @grpKeys ) {

    ## Remove any arrays from teh previously processed group
    ## that are below the interval of the next value - $INT
    shift @oldGrp while ( $next - $oldGrp[ 0 ] ) > $INT.

    ## Process items in the new array
    for my $i ( 0 .. $#{ $hash{ $next } } ) {

        ## against each of the (other) items in the new array
        for my $j ( $i+1 .. $#{ $hash{ $next } } ) {
            process( $i, $j );
        }

        ## and all of the items in each of the arrays 
        ## retained from the previous pass
        for my $g ( @oldGrp ) {
            for my $j ( 0 .. $#{ $hash{ $g } } ) { 
                process( $i, $j );
            }
        }
    }
    
    ## Add this array to the previously processed group
    push @oldGrp, $next;
}
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