Measuring a low AC Voltage with microcontroller
There are a few possible approaches: 


amplify the voltage with an AC-coupled amplifier and offset it to the middle of the ADC range. 
amplify the voltage with an AC-coupled amplifier and make an AC-DC converter (precision rectifier) as would be used in a DVM (this may will have more potential problems with noise being interpreted as signal)
amplify the signal with an AC-coupled amplifier and synchronously demodulate the output voltage by effectively multiplying it with the energization signal. This can be done in the digital domain using 1. or in the analog domain using analog circuitry. This is effectively a lock-in amplifier and can give you superior performance by acting as an extremely narrow-band filter, so most of the noise falls outside the passband.