I again talked to USCIS Customer Service today, they are also saying that TD is tied to the TN, the TD visa start date cannot be changed from Dec 01, 2006 to Nov 3, 2006. And I should have gone to POE to Change my starting date before Nov, 2, 2006.
So what you should have done is got her status changed from B to TD (Nov 3 to whatever your old TN expiry was) by filling out I-539. Then again, you should have sent her new I-539 along with your extension.
Now, if she is out of status, there is nothing you can do from within the USA.
What option do we have now?
-- Get her out ASAP and then request the re-entry visa by explaining your situation.
Does she have to leave immediately or can we apply for something from here?
-- Leave ASAP.
Is there any grace period to leave?
-- No. Once your I-94 expires, there is no grace period.
and will she face any problem while coming back on Dec 02, 2006 on TD visa as she over stayed past her visa here.
-- More her no. of "out of status days", more likely it is to face the issues. That's why I said, leave ASAP.