So, without reading the documentation for Alley and what to do with the different DXV codecs, I went balls to the wall and decided to convert everything to DXV3 HQ (using alpha only where applicable). I now find that many clips stutter/lag, which I'm guessing is due to the artifacts mentioned when going from DXV2 to DXV3 HQ. I have already deleted most of the older files.
Right now I'm converting the HQ to NQ to see if that resolves the problem, but a test run on a couple files didn't seem to make a difference. Any thoughts on how to fix this stupid mistake?