Hi Jatan,
Sorry, Im not a FPGA "doer", as I know is core=VccInt_am I correct Or is for you with VccAux too?
Otherwise, the first problem is physical acsessing & if you have it, than the over their writen "high side" current sensing; as Allegros ACS712 or others...
The ACS712 has onchip shunt resistor, nice small SMD IC, with 66 to 185 mV/A output sensitivity...(The ACS712 is provided in a small, surface mount SOIC8 package. the device is Pb-free, except for flip-chip high-temperature Pb-based solder balls, The device is fully calibrated prior to shipment from the factory. )
I think simplest physical access is at the dedicated voltage regulators outputs!
, here have you to insert the sensings electronic.
Rest is SW, that you have in same puls (takt) to convert with the ADCor makes some LP-filtering/integrating (avrg) for easyer conversion and so on.
K.