Coach
The rule as I was taught was "what would you do if there was no penalty." So, in your case, run ended in bounds, so without the clock stopping for the penalty the clock would have continued to run. Two other cases illustrate this. So, clock was running after 2nd down, and Offense throws an incomplete pass, but Defense gets called for Offsides (or Roughing the Passer). With your question, the clock should run because it was running on the last play. But the rule is what happened on 2nd down -- an incomplete pass. So, enforce the penalty and clock is stopped and does not start until snap because of the incomplete pass. Second case is Holding call on play the Offense scores a touchdown. Enforce the penalty, and clock starts on the snap because without the penalty, the clock would not run after a score -- because you would go to the untimed try.
Simple!