I was finally able to get it to work. I used the following command in my perl 
script to get it to work.

$output = `recover -d $destination -c $notesclient -t $nsrdate -a $restorepath 
2>&1`;

This was inside a loop then just printed the output variable to a file.
I was finally able to send all the output to a file, but the only thing I didnt 
like was the output didnt get sent till that one particular recover was 
completed. Good enough though.
Thanks

+----------------------------------------------------------------------
|This was sent by ess07 AT health.state.ny DOT us via Backup Central.
|Forward SPAM to abuse AT backupcentral DOT com.
+----------------------------------------------------------------------

To sign off this list, send email to listserv AT listserv.temple DOT edu and 
type "signoff networker" in the body of the email. Please write to 
networker-request AT listserv.temple DOT edu if you have any problems with this 
list. You can access the archives at 
http://listserv.temple.edu/archives/networker.html or
via RSS at http://listserv.temple.edu/cgi-bin/wa?RSS&L=NETWORKER