here's the rule:
Penalties – The clock will stop for penalties (immediately for illegal procedure and encroachment) or upon conclusion of the play for other penalties. If the clock was running when the penalty occurred, the officials will start the clock when the ball is made ready for play. If the clock was stopped when the penalty occurred the clock will remain stopped until the snap.
First -- the clock does not stop for procedure fouls -- since there is not one. There's illegal shift -- motion -- not enough on the line --- etc....and they are all live ball fouls and the clock keeps running until the play ends. On false starts and encroachments -- it's a dead ball foul and the clock is blown dead.
As Febref pointed out -- after the spike --which is an incomplete pass -- and by rule 3-4-3e-- the clock will start on the snap after a legal or illegal forward pass. What happened before that --clock running or not --is of no consequence. The spike kills it and it's in the book for a reason...black and white.