If using the system command is not working for you, then I'd suggest to use a system service instead. By the way, you don't need to call "root" and your password when using the command system.
I wrote a document about a similar subject that you might find of help. It will require some modifications but probably not many:
Regarding your second question, the user CMata_Intel wrote a very good example on how to "see" Linux info in the Arduino serial port, check Re: Battery supply monitor, it might be of your interest.