You can search external file system from within Alfresco.
Option 1. Move all the files from G:\ and X:\ into Alfresco and mount them using Alfresco CIFS. You can define more than one network share. So you can even use G:\ and X:\ to access the specific spaces with that content in Alfresco through CIFS.
Then search and permissions just work.
Option 2. Run Nutch standalone to crawl and index your file system. Create a separate application or AJAX app that calls through to both Nutch and Alfresco and displays the two sets of results.
Alfresco results will be filtered based on user's permissions.
How to filter Nutch results is something you need to check the Nutch forums.
Have you considered getting a Google Search Appliance?