Here's a simple recursive solution (read the comments for explanation):

#!/usr/bin/perl
use warnings;
use strict;

sub alternate {
    my ($id, $string, @changes) = @_;
    unless (@changes) {
        print "$id $string\n";
        return
    }

    # The variant with the original character.
    my ($bracket, $char) = @{ shift @changes };
    alternate($id, $string, @changes);

    # The variant with the alternative character.
    $string =~ /\(/g for 1 .. $bracket;    # Find the bracket.
    substr $string, pos $string, 1, $char;
    alternate($id, $string, @changes);
}


open my $STRINGS, '<', 'File1' or die $!;
open my $ALTS,    '<', 'File2' or die $!;

while (my $string_line = <$STRINGS>) {
    my ($string_id, $string) = split ' ', $string_line;
    # Count the bracketed parts.
    my $count = ((my $bare_string = $string) =~ s/[()]//g) / 2;

    my @changes;

    for my $bracket (1 .. $count) {
        my $alt_line = <$ALTS>;
        my ($alt_id, $pos, $orig, $alt) = split ' ', $alt_line;

        die "Out of sync: $string_id != $alt_id\n" if $string_id ne $a
+lt_id;

        my $char = substr $bare_string, $pos - 1, 1;
        die "Invalid char at pos $pos in $string_id: $orig != $char\n"
            if $orig ne $char;

        push @changes, [ $bracket, $alt ];
    }
    alternate($string_id, $string, @changes);
}
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It might be a bit too complex for a newbie, but the task is not really simple, either.