Let me get this straight, your entire injector calibration is done completely via FKKVS?
Regardless, every map has a purpose and should be used as designed.
It sounds like you need to start over on your injector and MAF calibrations and tune one peice at a time. I highly doubt your intake manifold is the problem.
KFKHFM corrects for intake PRE-MAF.
FKKVS is for correcting non-linear injector behavior which, if neccesary, should be mainly at low pulsewidths. Some injectors also have an upper non-linear region, but the injectors should be linear at part throttle.
You should be focusing on KRKTE, TVUB, and MLHFM.
What is the application? What is your MAF/intake setup?
Totally correct. Also note that IF you have installed a bigger throttle you have to recalibrate throttle airflow in function of throttle position