The biggest problem you will have is the bad resolution and accuracy of cells on top of the stack. With 48 alkaline cells your top voltage will be approximately 72V. If you reduce this to 5V, you need a 15:1 resistive divider, which will effectively reduce your resolution by a factor of 15 as well. With a 10-bit ADC in a typical PIC, even with perfect resistive dividers, your measurement resolution on the top cell will only be 70mV. That is not enough to get any meaningful state-of-charge (SoC) information.
Worse still, resistor mismatch and drifting over time and temperature, as well as variability in the analog mux switch resistance will introduce very large measurement errors. You will definitely have to use muxes with a very low resistance compared to the resistance of your dividers. Also, you will have to calibrate out the initial error of your dividers and use resistors with low temperature drift. Furthermore, to increase your resolution you can introduce a noise source on your ADC input and average out many consecutive conversions to get an effective higher resolution. However, this may make the total sweep time prohibitively because of the sheer amount of cells you are trying to measure. Also take into account that you need a fairly long settling time as you will be using high-value resistors for the dividers (to avoid sucking the batteries dry with all those resistors constantly attached).
Other ways to perform this measurement are not necessarily 'easier'. I designed such a system very long ago to monitor ultracapacitors in an electric race car, and used a Maxim high-voltage multiplexer that could switch any cell into a voltage-to-current converter (standard opamp circuit). This fed into a ground-referenced resistor that in turn fed into a standalone ADC. This system was very easy to expand to very high voltages, but it requires expensive high voltage multiplexers and is definitely more involved and more complex than just resistive dividers.