The flight logs are recorded on the SD card inside the flight controller. You can access them by downloading them with ground control software like Mission Planner, or by putting the SD card in your computer. http://ardupilot.org/copter/docs/common-downloading-and-analyzing-data-logs-in-mission-planner.html
In the log, the accuracy data is contained in the GPA category. In Mission Planner, it looks like this:
And yes, the logs can be parsed by scripts. The logs are in a binary format, but Mission Planner automatically converts and creates a plain-text .log version when you download them. Mission Planner also has a button to convert any log, or you can use any of these tools to do it yourself if you want.