What you are trying to do should be possible, but as you acknowledge, it will be a lot of work.
I think beyond the wiring and coding, you may have to map the A/D readings into something compatible with what you would get from an on-chip A/D pin, depending on bit resolution and the analog reference voltage, but this should be a linear relationship.
Another idea would be to repurpose some of the pins being used for existing stepper drivers to regain an analog input pin. You could do this by placing a header underneath one of the stepper driver cards to “steal” one of the pins, substituting one of the digital pins from the aux header. Of course you would need to re-map the pin assignments for the affected stepper, but this might be as easy as a simple change to Pins.h. A variation on this idea would be to make your daughter board plug into both the aux header and the slot for one stepper driver, then move the displaced stepper driver onto your board and re-map the pins there.
You can definitely get the Vin by tapping into the screw terminal connector. This is not as clean as getting it through the aux connector would be, but you probably wouldn’t want to be drawing all that power through traces on the controller PCB anyway. You will want to use reasonably heavy gauge wire to ensure it can carry the motor and heater current, and also make sure any traces on your board are sufficient.
At the risk of sounding discouraging, you can get an ATMEGA 2560 for about $10 and a RAMPS shield for $20, so replacing the controller is definitely something to (re)consider. You’ve probably already seen my dual extruder thread, which has more details about using the RAMPS board:
However you proceed, please let us know how you make out. Have fun!