I know what you experiencing , i have the same thing , although is getting better as the IAP map is getting complete and as i have change the EVT map. I think removing the CAT and exhaust valve, the demand for fuel at lower RPM is higher , once the IAP map is set, this problem is less . make sure setting the header length and diameter correctly then write the auto tune to the IAP and TPS map after 5-6 times of riding, then you will have smoother lower RPM.