Measure Battery Current via Shunt
There are many "high-side" current monitoring amplifiers which make this task much more easy and avoid cutting the ground rail to insert shunts.



Figure 1. The INA219 Zerø-Drift, Bidirectional Current/Power Monitor With I2C Interface is one of many. (Click for larger view.)

There are numerous version of similar devices - some built on hobby boards, etc. 

If you can use I2C then that should simplify your wiring, connections and reduce the amount of analog signal handling required significantly.