To address the problems you're having, I would manually create a timer, rather than using Time.time.
private var timeRemaining : float = 60.0;
function Update()
{
timeRemaining -= Time.deltaTime;
}
Using this approach:
you can subtract time in an Update loop you know will only get called when not on the main menu.
you can add to timeRemaining to extend the countdown.
If you'd rather use Time.time, you could use a few other variables to track bonus time and paused time, but I honestly think this way is simpler. Please ask if you have any questions!