Leave US after 240 days?

[wwjd]

It's hard to find the right answer to this question...

I have a (3 years) R1 Visa that expired January 12, 2009

A I-129 petition for extension was sent in October 2008 (still pending)

My I-94 form says arrive: Jan 02 2009 & Departure: Jan 02 2012

Now...

The C1 customer guide "How Do I…Extend My Nonimmigrant Stay in the United States?" have a paragraph (What if I file on time but USCIS doesn’t make a decision
before my I-94 expires?) mentioning MAXIMUM 240 days...

http://www.uscis.gov/files/article/C1eng.pdf

1) Is that 240 days from my visa (JAN 12, 2009) expired?

2) Is that 240 days from my first entrance (May 10, 2006 + 3 years) to USA on my R1 Visa?

3) Is that 240 days from my I-94 (JAN 02, 2012) expired?

I have had so many different answers... PLEASE help...