Or:

use Data::Dumper;

use strict;
use warnings;

my $array = [
    'foo bar quux bam',
    'foi bir quix bim',
    'foe ber quex bem',
    'foa bor quax bom'
];

my $ins =   '4 A -4 C -4 B 2 D';

my @ins = split(/\s+/, $ins);

my @result;
for my $line (@$array) {
    my @pieces = split /\s+/, $line;
    my @joined;
    for my $j (0 .. $#pieces) {
        push @joined, $pieces[$j];
        push @joined, $ins[$j* 2 + 2] unless ($j == $#pieces);
    }
    push @result, join(" ", @joined);
}

print Dumper(\@result);
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