The grinding and bucking has all but stopped, there's an occasional misstep but no big deal. I'm at 2400mi and it appears the computer has figured out how to shift, I just hope there was no permanent damage.
That being said, this thing is now a pleasure to drive. It actually feels quite peppy for a little four banger, aside from the occasional extremely late shift, this thing can really get up and go. It pulls nicely on the highway even at high speed, that was a very pleasant surprise. All in all, I'm very pleased with the Focus.