Update 4/28/14: A new version of the Office Customization Tool (OCT) has been released as part of the Office 2013 Administrative Templates to address this issue.  You can download the OCT from http://www.microsoft.com/en-us/download/details.aspx?id=35554.  Once downloaded double-click the executable to extract the contents which includes the Admin folder.  Copy this folder over the existing \Admin folder in your Office source.

Create an MSP file to deploy Office 2013 w/ Service Pack 1 using the newly downloaded OCT.  If you want to use an existing MSP file you will need to Import the existing MSP file into the newly downloaded OCT and then save the MSP file.  Not importing an existing MSP file may cause the OCT to fail.

 
After installing Office 2013 with Service Pack 1 from the Volume Licensing Service Center (VLSC) with a customized MSP file using the Office Customization Tool (OCT), Lync and OneDrive for Business are not installed.

We are currently investigating the issue and will provide an update soon.  In the meantime, please use one of the following workarounds:
 

1. Use the Updates folder on the original RTM release and the publically available Service Pack 1 MSP files: http://support.microsoft.com/kb/2817430.

For further information on using the Updates folder to install Office updates, refer to the following Microsoft article: Deploying software updates with an initial Office 2013 installation

2. Use the config.xml file to add Lync and OneDrive post install of Office 2013.  To accomplish this, edit the config.xml file to have the following:

<Configuration Product="ProPlus">

               <Display Level="none" CompletionNotice="no" SuppressModal="yes" AcceptEula="yes" />
               <OptionState Id="GrooveFiles2" State="local" Children="force" />
               <OptionState Id="LyncCoreFiles" State="local" Children="force" />

</Configuration>

Note - this issue also applies to Excel Add-ins Power Map and PowerPivot.  If there is a need to install these add-ins you can do so by adding the following to the config.xml file:

               <OptionState Id="ExcelAddInPowerMapFiles" State="local" Children="force" />
               <OptionState Id="ExcelAddInPowerPivotFiles" State="local" Children="force" />

Once the install of Office 2013 with SP1 has completed, run the following command-line:

<path>\setup.exe /config <path>\config.xml

For further information on using the Config.xml file in Office 2013, refer to the following Microsoft Article: Config.xml file reference for Office 2013

Background:

The SP1 release of Microsoft Office 2013 Click-to-Run for Office365 offers a new Update Now feature on the File | Accounts (backstage) page of each Office application:

More Information:

This new feature allows users to check for and install updates for Office on demand.  Under the hood, there is a new OfficeC2RClient.exe file that makes this possible.

Outside of this user interface, the OfficeC2RClient.exe can be run from an administrative command-prompt by constructing an appropriate command-line in the following format:

%Program Files%\Microsoft Office 15\ClientX86 | ClientX64\OfficeC2RClient.exe /update user variable1=value variable2=value … variableN=value

Where the variables are optional settings and based on the following table: