Cheers for all the tips.
OK, with the assistance of 13 year old Chasiette, the string method showed up that the notches on the swingarm are out by about 1.5mm, meaning the right front edge of the tyre was cocked in a bit. That hadn't shown up by the lie down and squint method or countin threads, somehow. Lesson 1: don't be a lazy git. I've marked one face of each adjusting nut so I can keep them in sync.
Also using the tip of the ScottOiler as a reference, it appears to me that the rear sprocket has actually got a bit of lateral variation i.e. either it's not perfectly flat or the fitting is a bit out somehow... It's around 0.5mm variation I'd guess.
Now I just need to find a large friend to check tension and I'll check it again in another few hundred to see if it seems any worse.
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