I've still got issues with the rear brakes, with the left hand side dragging and an ineffective handbrake. A lot of problems can be diagnosed with careful visual inspection, so that's what I did. I thought disk runout might affect the self-adjusting mechanism, so I checked it with a dial gauge. It measured 0.2mm max at the disk edge, and this seems to be caused by the hub face being slightly out of true.
The handbrake return springs were bent, so I've ordered a new pair. It turns out that the modified levers stop the mechanisms from returning to their 'off' positions, so a little modification with a hacksaw is in the pipeline.