I took the bike out for a short test today, and have a few observations.
1. Changing gear remained very clunky, but seemed marginally better when on the large front ring. In every case shifting appeared worse as I moved down the cassette.
2. The chain felt very tight on bigger gears - but this may be a false perception since I was concerned about it snapping the way it did yesterday.
3. The rear disc rotor was making a very loud screeching noise whenever I stopped pedalling - this stopped after a couple of miles. It's a new rotor, since I went from 6 bolt to center lock as part of the wheel changeover. I didn't know if this is related in any way to the gears issue
I've attached some more photos, but not sure if they help.
Thanks