How to monitor the voltage of a bunch of batteries using Arduino?
You can use analog mux/demux iCs such as CD4051 (8 channels to 1). In fact, you can use 5 of them for the 36 batteries (you'd be left with 4 extra channels) and connect each to one analog input, and then connect all three control pins of each to the same three digital pins outputs in the Arduino. Then you'd be binary counting from 0 to 7 on those three pins and reading all 5 analog inputs on every cycle.

I also recommend using some op-amp to shift the voltage range of 2.8V - 3.6V to 0V - 5V. This way you'd get better precision and with some simple math on the Arduino you'll be able to get a much more accurate reading.