It works for your test case :)

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1196126

use strict;
use warnings;

my (%waiverhash, @waiverstar);

open my $w, '<', \<<END or die;
c4a_123,350.00,3300.00,"Justification","Waived,by","Waived,Date","Appr
+oved,by","Approved,date"
c4emib_*,250.00,2000.00,"Justification","Waived,by","Waived,Date","App
+roved,by","Approved,date"
END
while(<$w>)
  {
  my ($name, $target, $adhust) = split /,/;
  if( $name =~ s/\*/.*/g )
    {
    push @waiverstar, [ qr/^$name$/, $target, $adhust ];
    }
  else
    {
    $waiverhash{$name} = [ $target, $adhust ];
    }
  }
close $w;

while(<DATA>)
  {
  my ($name, $target, $adjust) = (split)[1 .. 3];
  if( $waiverhash{$name} )
    {
    $target == $waiverhash{$name}[0] and $adjust <= $waiverhash{$name}
+[1]
      and s/VIOLATED/WAIVED/;
    }
  else
    {
    for my $star ( @waiverstar )
      {
      if( $name =~ $star->[0] )
        {
        $target == $star->[1] and $adjust <= $star->[2]
          and s/VIOLATED/WAIVED/;
        last;
        }
      }
    }
  print;
  }

__DATA__
f1    c4a_123           350.00    3251.94   -2901.94  (VIOLATED)
f1    c4b_123           350.00    2419.08   -2069.08  (VIOLATED)
f2    c4emib_2060       250.00    2000.00   -1750.00  (VIOLATED)
f2    c4emib_2061       250.00    2000.00   -1750.00  (VIOLATED)
f2    c4emib_2062       250.00    2000.00   -1750.00  (VIOLATED)
f2    c4emib_2063       250.00    2000.00   -1750.00  (VIOLATED)
f2    c4emib_2064       250.00    2000.00   -1750.00  (VIOLATED)
f2    c4emib_2065       250.00    2000.00   -1750.00  (VIOLATED)
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