Question: When the train is put into reverse, Bronson and the major jump off. The Indians get into the box car then the train stops. Who stopped it?
Question: How did Sonny know that the black limo driver was a cop?
Answer: He didn't. He just assumed the cops would try something like that, substituting a cop for the real driver. What he didn't anticpate is that they had substituted cops for everyone around the bus when it arrived, and when he replaced the black driver he would have to (unknowingly) pick a cop, regardless. Incidentally, this part of the story is completely factual, it actually happened that way.
Answer: Ben Johnson and Charles During. Their characters had guns pointed at them, they stopped the train suddenly to knock them off balance. As soon as Bronson and the Major jumped off the train, Johnson and During took control of the engine.