but it would be nice if someone could point out a couple of more flaws with this idea
I will then have resistors being connected to gnd using low Rds(on) fets that's controlled by the mcu, this will lower the Vref dramatically thus making it possible to measure uA's and mV's.
Is rubbish because there is a minimum size for the reference voltage of all A/Ds the arduino's is 1V. This is governed by the noise / hysteresis of the comparator.
As for the shunt resistor I guess I would have to make the MCU change this out using fets as well as the voltage drop across a 0.1Ohm resistor isn't much if 1uA goes through it, and the heat dissipation would be too much to handle if 10A goes through a 10Ohm resistor.
The FETs need to be good so that their on resistance doesn't overwhelm the shunt resistance.
The last thing that would really top this off is if the voltage and current can be measured anywhere in the circuit, not just as ground as a referance, but I'm not sure how that is accomplished (how does a DMM do it?).
By having two leads and being battery powered and so isolated from the circuit it is measuring.
The reason I think I need two mcu's is because I need to individually set Vref for each of them so that one handles the voltage, the other handles current.
No, if you do need two referance voltages then switch them.
Also, how happy will the MCU be if I connect Vref to a really low voltage (let's say 1mV)?
I can't find any information about this in the datasheet.
Table 28.7 Page 323, minimum voltage 1V.