My main audio computer has nine HDD installed. When I start a clean audio folder routine, it takes quite a bit of time
because the routine is forced to walk all of the drives looking for project files. For whatever reason, the search will
frequently freeze at some point (SQL server seems to be a popular spot) and I end up doing the work manually. Is it
possible to add another filter to the script for the routine to restrict the search to a particular drive? There is only one
drive on the machine that contains project files.

Check out Cakewalk Audio Finder (CWAF) tool; it's much faster, more flexible and powerful in terms of what it searches, what it tells you about what it finds, and how orphaned files are handled. See this post:
 
http://forum.cakewalk.com/FindPost/3023681