I would like to eliminate the USB battery pack, and run both the motors and the RPi3 from the Dagu battery pack (6xAA). Can I achieve this by using a step down regulator (https://www.pololu.com/product/2851 or similar) connected to the RPi3 microUSB port? Should I take some precautions, in order not to fry my RPi3?
You should be able to power the Raspberry Pi 3 from the D24V50F5 voltage regulator and you can connect it to the Raspberry Pi micro USB port through a cable. If you tell me more about your plan to power your Raspberry Pi, I might be able to give you more advice.