The flavour of MAVLink that ardupilot uses can be used to get the information that you need and to send commands too: When you have the example working then you should read up on MAVLink, the protocol that ArduPilot uses to communicate with external devices.
You may also need to read up on Serial port protocols to set the Baud rate, parity and stop bits correctly ( Note this is done automatically by USB, but you will need to get this right for your non-usb ArduPilot to Arduino serial link) I would start by getting the ArduPilot to get some basic output to your PC via its serial port ( or USB cable which acts like a serial port) Try running one of the example sketches on your ArduPilot hardware. I would ignore I2C to start with and use USART to begin with.
