The clock stopped due to the ball becoming dead per the fourth-down fumble rule. When a player other than A11 recovered the fumble, the ball would have returned to the spot of the fumble. However, since B would not be next to snap the ball with the penalty, the game clock starts on the ready-for-play signal. A 1/G , B-2.5, GC RFP, PC 25.
The ball is dead by the 4th down fumble rule, but that is not why the clock stops. You won't find any reference to the 4th down fumble rule in Rule 3. Rather, in this example, it will be:
1) because of the 'apparent' touchdown (before determining that the ball will be returned to the spot of the fumble, which results in the award of a first down to Team B);
2) to award Team B a first down;
3) to complete the penalty.
The purpose of this question is to determine when the clock will next be started. For 1), it would start on the snap. For 2), it would start on the snap. For 3), it would start on the Referee's signal.
Redding/Shaw may say that there was no 'apparent TD,' because of the 4th down fumble rule, so we know there will be no score. But, we could say the same thing about an 'apparent' TD with a live-ball foul by the scoring team, i.e., we know there will be no score. And we know that the clock will next start on the snap in that circumstance.
If the clock was stopped to complete the penalty, then we know the clock will next start on the Referee's signal, because Team B will NOT next snap the ball.
I don't have an authoritative answer. I'm guessing RR/SS would rule that the clock stopped to, ostensibly, award a first down to Team B, but, following the penalty, B will NOT next snap the ball, so the clock will next start on the Referee's signal.
But there is no clear answer to that in the Rules, Interpretations, or Bulletins.
Robert