Starting and Stopping the Clock

[Niner]

With 12 seconds remaining and the clock running in the 4th quarter, team A runs the ball to B’s 5. They immediately (after the ready of play whistle) line up and the quarterback takes a direct snap and legally spikes the ball to stop the clock; however, a) there is an illegal motion penalty on A on the play, or b) several interior linemen were unable to get set. If B declines the penalties, when do you start the clock and if it expires before A can snap, do you extend. If B accepts the penalty when would you start the clock and if you start the clock and it expires before A can snap the ball, is there an extension?