Here are some notes on customising exports created via the BizTalk Administration Export MSI file.

Before creating the export, add any externally referenced .Net assemblies by adding them as a resource in the BizTalk Application's Resources folder:

This will allow you to include the added resources in your export and will add them to the Global Assembly Cache during installation.

This is also a good means of deploying binding files for different environments.

Also, verify the Destination Location of all resources are set to install in the deployment folder.  The following assembly

Should be modified so it will install in the installation folder:

A tool like Orca (available in vista SDK) can be used to modify the default deployment folder by changing the manufacturer property.  The screen below shows the property to be modified:

Just some notes...