i did try to calibrate individually. when i tried IF Step Amp it also report Input Att failure. the other item will report HS ADC failure (the problem becomes worse). i did Total gain cal it success without warning but...
Did you confirm that the 30 MHz reference is on frequency and at the correct level?
i checked with my KC901V in SA mode, the 30MHz CAL out is spot on at -10dB... currently R3465 reads about -5dB lower than that. with failure to complete all calibration, the R3465 reading is a bit off. and unluckily LPRO101 Rubidium that i bought from a member here also playing up, cannot locked when i need it most

i believe i need to check further downstream, next to Att is YIG BPF model Advantest TOP2302X, not sure what this one does, i can find in the net stating its YIG Filter, but no datasheet. band pass filter of what? is this IF stage? what should i expect on the output? see attached.