It’s a start, but this seems to be the technique to use for multi-instance installers built using WiX:
1. Have bootstrapper (script? app?) programatically create a transform based on passed in instance name.
2. Transform should store some info in a custom table and set the GUID of the product to something unique. Set default installation directory too?
3. Install needs to save GUID of product/instance to somewhere in the registry so that instances can be listed and selected in (1).