Ah, I see. Haven't been to Nar Shaddaa yet, but I've added Mira's jacket through console commands and still no ability to upgrade it. Yes, the files are saved in the Override folder. I at least knew that much when I started messing around.
I would start a new game and go from there, but I've never cared for Peragus or Citadel Station, and I've just recently gone through both of them. Suppose I can leave the files in and see if they do anything on my next playthrough, but that's a long ways off.
Oh well. Thanks anyways, I think.