There seems to be a huge difference in performance when running the scan locally as opposed to via UNC.
Testing Scenario #1 (Scan over UNC from index server)
index srever = index server
access node = index server
875GB took 25 minutes
Testing Scenario #2 (Scan local on fileserver)
index server = index server
access node = fileserver
875GB took 44 seconds
To get this configuration working, I had to install the MA and index server packages on the fileserver and then create a new index server via the commserve. I still specifed the same index server as in testing scenario #1. Although a new index server was created on the fileserver, it doesn't appear to be using the directory structure at all, which is kind of what I expected.
* incremental crawl was unchecked for both tests