As to why the surging when warm, it is possible that when cold the bike is running a little ratty and not burning all its fuel. After getting up to temp, the rings might be sealing better and the bike could be pulling more vacuum as it is generating more power at idle.
If you have a spare carb body, it is worth a try. I have heard of the slide sticking on high mileage 4 strokes, but 4 strokes tend to pull a lot higher vacuum at idle than two strokes.
BTW, my KDX250 used to surge when trying to maintain a constant rpm on the highway, but I attributed it to the powervalve 'hunting' between closed an partly open. The PV should not be impacting how the bike idles, but if the carb swap doesnt' help, you might want to make sure your KIPS valves are closing all the way.