i personally think your HHT is too high for 400F and you get too much momentum and thus the overshoot. since you go so far over, LHT is in control for too long and then you go way under setpoint. With your flue adjusted to a better spot, have you gone back to trying factory settings of 10/100?
here is the other thing that I try when I start having these kind of problems... i set my LHT and HHT at the same value. Theoretically this should produce a constant feed rate. for high temp cooking, this will define your HHT, for low temp cooking this will define your LHT. Then tweak the other value to provide your buffer. The LHT on high temp cooking is your "pilot light" the HHT on low temp cooking is your safety net if ambient conditions or other variables change and you need to kick things in the butt.