This morning I decided to run a full scan, just for maintenance, and the scan only took 17 some-odd minutes, update and all, with no threats. My being used to scans taking hours before having to wipe my HDD and re-install windows 7, I decided to watch it do another full scan or two. Now it seems to complete in less than 3 minutes with no threats, which I find extremely odd with about 785 gigabytes on my computer currently, even with it already being up-to-date. As far as I can tell, the file size is unrestricted on the full scan when checking it’s options.
Welcome to the forum Crazy_Alan. 
It sounds like you are running CIS version 6? Version 6 builds a database of safe files, so it is normal for subsequent full scans to be considerably shorter than the initial scan.
I believe I am using whatever is the most recent version, which I do not see where to check that. Does the active scan prevent the possibility of “safe” files from being infected? And is there a way to scan those files anyway, in case I need it?
Yes, the AV scanner and the Behavior Blocker should help ensure that nothing infects those files. And if the files change in some way, they are re-scanned.
I don’t know if it’s possible to scan these files anyway.
I think that when you disable Enable scanning optimizations the AV will scan all files like it used to do.