How to include secondary drives' files into 'All My Files' feature
'All My Files' is a Smart Folder, that is, a saved Spotlight search, named myDocuments.cannedSearch:



and located in /System/Library/CoreServices/Finder.app/Contents/Resources/MyLibraries. You probably shouldn't modify it, as it is a system file.

However, you can create your own Smart Folder using 'All My Files' as a template:


Select 'All My Files' and click 'Show search criteria':


Choose 'This Mac' to search the entire computer:


Click Save and specify a name, for example 'All My Items Everywhere', and a location for your Smart Folder (the default in ~/Library/Saved Searches should be OK).

The Smart Folder will appear in the sidebar.
Select 'All My Items Everywhere', right click and arrange by kind:



to get a similar output as 'All My Items': 




The downside of creating your own Smart Folder is that you can't configure the Finder so that new windows display 'All My Items Everywhere'.