OK I now have a licensed app on VDI - this was achieved by using the AddPackage script command in the DeploymentConfig.XML and dropping the UserConfig XML when importing the sequence.
The only issue now remaining is when I try to create PDF's from DOCX/XLSX (works fine for TXT files) - I get the following error. Is this to do with (the lack of) interaction with Office 2013 or is it due to having a virtualised Adobe PDF Printer inside the sequence?
COM Integration Mode is set to
<COM Mode="Integrated">
<IntegratedCOMAttributes OutOfProcessEnabled="true" InProcessEnabled="false" />
</COM>
Object Interaction is set to
<Objects Enabled="false">

One need install the supplementary App-V MSI Downloads on the user’s machine which contain Acrobat’s integration points for applications such as:
- MS Office Integration - Context Menu and In-App Acrobat Ribbons.
- Mails Integration - MS Outlook and Lotus Notes will start showing Acrobat Features.
- Adobe PDF Printer - Allows the user to print any file to Adobe PDF.
- Web Capture - Allows the user to be able to convert a webpage to Adobe PDF inside the Browser.
- Registers necessary fonts on the client which will be used by the virtual application.
The same can be downloaded from http://www.stage.adobe.com/devnet-docs/acrobatetk/tools/AdminGuide/appvacrobatDC.html#msi-downloads
Please note this MSI has been designed specifically with machine based deployment. This has not been validated and tried with the user specific deployment.