#1: I think you mean B's 3 yard line.
#2:
Don't think you can use your concern over clock management to ignore a foul. This is HS football, you can't assume A will make the roughly 35 yard FG to TIE the game. Our job is not to predict the future. You deal with the issue at hand.
#3: If this is a real life play, how aggressive was your crew's dead ball officiating in this instance. This tight, we don't need to be letting A lay hands on B or vice versa. If there was no time to prevent it then A has to suffer the consequences, which will be 15 yards further back from a scoring opportunity.
3-4 ART. 6 . . . When a team attempts to conserve or consume time illegally, the referee shall order the clock started or stopped.
This give you discretion. If B is slow to get off the pile, you are covered. If A's illegal act is allowing to conserve time, you are also covered.