1000 miles later nothing has broken, fallen off or worn out. Considering how worried I was when I first saw the inside of the engine, that's a decent result. The one nuisance is a tendency to stall approaching junctions, even though the bike ticks over and pulls away perfectly well.
Another owner, Simon Relph, says they all do that, and the best cure is a new carb from an XR600. I've also talked to the previous three owners and they all say the pre-rebuild bike stalled like that for years. The question is, why?
Assuming the ignition and valve clearances are fine, and taking Simon's observation that a new carb fixes it, I decided that the carb must still have some problem despite professional cleaning. Replacement isn't cheap, and the carb isn't worn, so it must be possible to put whatever is wrong right. Maybe the design makes some of the small bleed drillings incredibly prone to gumming up?
I stripped the carb down and spent a long time with carb cleaner and compressed air, trying to ensure the four pilot drillings were clear. These are the holes which the pilot adjustment screw covers or uncovers as you screw it in and out. I concentrated on these bits because when I tried to set the carb up originally after the rebuild this screw made virtually no difference.
Carb reassembled and fitted, fire it up – still no good.
I have found some extremely small drills. They may come in handy.