use warnings;
use strict;

open my $schedule, '<', 'Schedule';
my %schedule;
$schedule{$_} = 1 while (<$schedule>);
close $schedule;

open my $wave,        '>', 'Wave'        or die "Can't open 'Wave': $!
+";
open my $keywords,    '<', 'Agents'      or die "Can't open 'Agents': 
+$!";
open my $search_file, '<', 'Definitions' or die "Can't open 'Definitio
+ns': $!";

my $scheduleData = <<SDATA;
SCHEDULE OTHER_NAME
DONTCARE
NOTIMPORTANT
:
MNDJWIEL#DIFFERENTDATA 
 OTHERDATA
 NOTIMPORTANT
END
SCHEDULE NAME_I_WANT
DONTCARE
NOTIMPORTANT
:
MNDJWIEL#OTHERDATA
 OTHERDATA
 NOTIMPORTANT
END
SDATA
my $agentData = <<ADATA;
HSJEKDIE
MNDJWIEL
NSKQI
OIFNHDU
H3KID
ADATA
my $defsData = <<DDATA;
MNDJWIEL#OTHERDATA
 SCRIPTNAME "JKASDHAJSDHAKJDAS.cmd"
 DESCRIPTION "NOTIMPORTANT"
OIFNHDU#UNIMPORTANT
 SCRIPTNAME "JKASDHAJSDHAKJDAS.cmd"
 DESCRIPTION "SOMETIMES HAS AGENTNAME OIFNHDU"
NSKQI#SOMETHINGHERE
 SCRIPTNAME "JKASDHAJSDHAKJDAS.cmd"
 DESCRIPTION "NOTIMPORTANT"
HSJEKDIE#DOESNTMATTER
 SCRIPTNAME "SOMETIMES HAS AGENTNAME HSJEKDIE"
 DESCRIPTION "NOTIMPORTANT"
DDATA

open my $schdIn, '<', \$scheduleData or die "Can't open 'Schedule': $!
+";
my %scheduleMatch = map {chomp; $_ => 1} <$schdIn>;

open my $agentsIn, '<', \$agentData or die "Can't open 'Agents': $!";
open my $defsIn,   '<', \$defsData  or die "Can't open 'Definitions': 
+$!";

my $agentsList  = join '|', map {chomp; qr/\Q$_\E/} <$agentsIn>;
my $agentsMatch = qr|\b($agentsList)\b|;

while (defined(my $defLine = <$defsIn>)) {
    chomp $defLine;

    if ($defLine =~ $agentsMatch && $defLine !~ /(SCRIPTNAME|DESCRIPTI
+ON)/) {
        my $lineout = $defLine;
        my $flag    = $scheduleMatch{$defLine} ? 'Yes' : 'No';
        print "$defLine | $flag\n";
    }
}
[download]

MNDJWIEL#OTHERDATA | Yes
OIFNHDU#UNIMPORTANT | No
NSKQI#SOMETHINGHERE | No
HSJEKDIE#DOESNTMATTER | No
[download]

MNDJWIEL#OTHERDATA | Yes | NAME_I_WANT
OIFNHDU#UNIMPORTANT | No | Missing
NSKQI#SOMETHINGHERE | No | Missing
HSJEKDIE#DOESNTMATTER | No | Missing
[download]

use warnings;
use strict;
my $scheduleData = <<SDATA;
SCHEDULE OTHER_NAME
DONTCARE
NOTIMPORTANT
:
MNDJWIEL#DIFFERENTDATA 
 OTHERDATA
 NOTIMPORTANT
END

SCHEDULE NAME_I_WANT
DONTCARE
NOTIMPORTANT
:
MNDJWIEL#OTHERDATA
 OTHERDATA
 NOTIMPORTANT
END
SDATA

my $defLine = 'MNDJWIEL#OTHERDATA';
open my $schdIn, '<', \$scheduleData or die "Can't open 'Schedule': $!
+";
my @values=();
while (<$schdIn>) {
  if (/(^SCHEDULE)(.*)/) { # SCHEDULE SCHEDULENAME, I only want the na
+me. 
    push(@values, $2);
  }
  if (/$defLine/) {
    print $values[-1];
    last;
  }
}
[download]

NAME_I_WANT
[download]

So something like this:

use warnings;
use strict;

my $scheduleData = <<SDATA;
SCHEDULE Unwanted
mu1
mu2
Nancy#mu3
 mu4
 mu2
END
SCHEDULE Wanted
mu1
mu2
Mindy#mu4
 mu4
 mu2
END
SDATA

my $agentData = <<ADATA;
Harry
Mindy
Nancy
Orlon
ADATA

my $defsData = <<DDATA;
Mindy#mu4
 SCRIPTNAME "doit.cmd"
 DESCRIPTION "mu2"
Orlon#mu5
 SCRIPTNAME "doit.cmd"
 DESCRIPTION "SOMETIMES HAS AGENTNAME Orlon"
Nancy#mu6
 SCRIPTNAME "doit.cmd"
 DESCRIPTION "mu2"
Harry#mu7
 SCRIPTNAME "SOMETIMES HAS AGENTNAME Harry"
 DESCRIPTION "mu2"
DDATA

open my $schdIn, '<', \$scheduleData or die "Can't open 'Schedule': $!
+";
my %schedules;
my $scheduleName;

while (defined(my $line = <$schdIn>)) {
    if ($line =~ /SCHEDULE\s+(\S+)/) {
        $scheduleName = $1;
        next;
    }

    next if $line !~ /(\S+)#(\S+)/;
    ++$schedules{$1}{$scheduleName};
}

open my $agentsIn, '<', \$agentData or die "Can't open 'Agents': $!";

my $agentsList  = join '|', map {chomp; qr/\Q$_\E/} <$agentsIn>;
my $agentsMatch = qr|\b($agentsList)\b|;
my $wantedSchedule = 'Wanted';

open my $defsIn, '<', \$defsData or die "Can't open 'Definitions': $!"
+;

while (defined(my $defLine = <$defsIn>)) {
    chomp $defLine;

    next if $defLine !~ /$agentsMatch#/;

    my $lineout = $defLine;
    my $flag    = $schedules{$1}           ? 'Yes'    : 'No';
    my $wanted  = $schedules{$1}{$wantedSchedule};

    $wanted = $wanted ? " | $wantedSchedule" : '';
    print "$defLine | $flag$wanted\n";
}
[download]

Prints:

Mindy#mu4 | Yes | Wanted
Orlon#mu5 | No
Nancy#mu6 | Yes
Harry#mu7 | No
[download]

My eyes don't parse a wall of uppercase text so I changed strings to something I could work with. I also removed the irrelevant file opens and the code building %scheduleMatch from an external file. It is important to trim out needless code and errors to focus just on the task at hand (see I know what I mean. Why don't you?).

The key is to improve the parsing of the schedules data so that we have both the agent name and the schedule name together in the schedules hash. Then the test in the loop processing the defs data becomes trivial.

Update: remove duplicated lines at the start of the example code (bogus copy and paste :-( ).

Optimising for fewest key strokes only makes sense transmitting to Pluto or beyond

Thanks, that looks a lot cleaner, I think I understand everything except the schedule parsing, in your example you're manually setting $wantedSchedule to 'Wanted', but in order to work as intended the script will need to take the variable output of I think $lineout which should be the info it gathered from $defsdata to see which schedule name to pull from $scheduleData, at least that's how it looks but then I don't know what your testing in the $wanted line above.

It's late and my laptop is off so I'll take a real look in the morning, not going to figure anything out on my phone with tired eyes.

I really appreciate the help though!

Fresh eyes didn't help much lol, I think perhaps I didn't explain the point of merging the scripts adequately.

The value that's printed in $defLine is the full line found in $defData after finding matching line in $AgentData, that seems ok. The $flag (yes/no) is telling me if that $defLine is also found in $scheduleData and if it is, then also scroll up and tell me the last matched regex capture for schedule name. We can't really scroll up, that's why I was using the look behind, It looks like you're putting that in $scheduleName but since it's being iterated before you go through $defData I don't understand the code suggestion as we don't know what we're looking for at that step.

The result looks ok in your example but it wouldn't actually work without setting the static variable in $wantedSchedule which I can't do because that needs to be dynamic data from the above, my example was static in the second script because I didn't know how to get the data out of the first one, but that's what I was asking for additional assistance with, I'm not sure I was clear or maybe I don't understand your proposal.