If you would like to manually assign a PIN number to a user in Lync, please follow the steps below:

1. Login to your Lync Front End Server
2. Open up the Lync Server Management Shell
3. Execute the following command
   1. Set-CsClientPin -Identity "DOMAIN\user" -Pin 123456

The technet article defining all the parameters of this command can be found here: http://technet.microsoft.com/en-us/library/gg398929.aspx