Don't overdo the <code> tags thing! Just include the code in it and not the text of the node.

Now on to the problem.

I'm quite sure the program doesn't do what you think it is doing.

To make matters clearer I have pared down the program to its bare minimum:

#!/usr/bin/perl -w
use strict;

my $CF = "watch process procAlive 'bgs' 18 0x2 60 'Production Critical
+: bgs failure. Restarting bgs' '/opt/EMPsysedge/bin/sysedge.sh'";

my $file = do { local $/; <DATA>};
s/^watch.*?'bgs'.*?sh'$//;
s/^(watch.*?'cron'.*?sh'$)/$1\n$CF\n/;
print $file;

__DATA__
watch process procAlive 'cron'      1 0x2 60 'Production Critical: cro
+n failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'inetd'      2 0x2 60 'Production Critical: in
+etd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'sendmail'  3 0x2 60 'Production Critical: sen
+dmail failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'syslogd'    4 0x2 60 'Production Critical: sy
+slogd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'automountd' 5 0x2 60 'Production Critical: au
+tomountd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'xntpd'      6 0x2 60 'Production Critical: xn
+tpd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'itaagtd'    7 0x2 60 'Production Critical: it
+aagtd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
[download]

Now you see that you read as one string the whole of each file into $file and then you operate your regexen on the default variable $_ which however you did not load with anything beforehand, hence the Use of uninitialized value warnings and finally you print the unchanged $file back to disk.

Don't try to be too clever and do it all at once! You need to do two things:

1. remove the line with bgs in it; and
2. add the $CF line after the line with cron in it.

As these are two separate things let's do them separately and as the unit on which you work is the line, let's do it line-by-line.

#!/usr/bin/perl -w
use strict;

my $CF = "watch process procAlive 'bgs' 18 0x2 60 'Production Critical
+: bgs failure. Restarting bgs' '/opt/EMPsysedge/bin/sysedge.sh'";

while (<DATA>) {
    next if /bgs/;              # skip printing the line with 'bgs'
    print;                      # print the line just read in
    print "$CF\n" if /cron/;    # add '$CF' if we just printed the lin
+e with 'cron'
}

__DATA__
watch process procAlive 'cron'      1 0x2 60 'Production Critical: cro
+n failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'inetd'      2 0x2 60 'Production Critical: in
+etd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'sendmail'  3 0x2 60 'Production Critical: sen
+dmail failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'syslogd'    4 0x2 60 'Production Critical: sy
+slogd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'automountd' 5 0x2 60 'Production Critical: au
+tomountd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'xntpd'      6 0x2 60 'Production Critical: xn
+tpd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
watch process procAlive 'itaagtd'    7 0x2 60 'Production Critical: it
+aagtd failure. Call USA POC' '/opt/EMPsysedge/bin/sysedge.sh'
[download]