I missed this response, but I think I've answered the questions throughout the post. But if not I'll give it a shot now.

The database doesn't exist yet, and I need to do the work as a proof of concept. So once the database exists, the script will be changed to point there instead of the files.
Binaries are just a presence/absence representation of an attribute. They are calculated from a series of raw values by evaluating the relationships of those values a few different ways.
I'm all for the database doing the calculations if it can. I'm in completely unfamiliar territory here, so recommendations are appreciated.