the AFC/FTC is not an exact science. it's just a basic piggyback. it's map table is only RPM and pressure. theres no way to fine tune for part throttle. so if you are running bigger injectors, your part throttle tune is going to suck. especially if you can hit full boost at like half throttle, like i do, it's going to be rich as s*** and theres nothing you can do about it except deal with it.
if you don't hit full boost under a decent load, it might run a little smoother.
you can try raising the activation pressure of output b to have the stock ECU tune part throttle since it factors in different TPS % at the same RPM and pressure.. I never tried this, i just left my output b at 0.1 psi
make sure output B is a few PSI LOWER than the max boost you run. do a datalog run and see where your boost is at through the whole run.