Why is the head welder Ned giving the press conference at the end? Forgiven because he is just that awesome.
Actually, "he's just that awesome" is the reason he's giving it - he's just played a major role in stopping a runaway train with explosives. It's also implied that he's being interviewed and not heading the conference because when it's asked what caused the whole incident, someone else steps up.
Also, the scene begins with a reporter explicitly directing the next question to him.
How'd he get into a suit?
It's implied time has passed - enough time for a press conference to be set up, and for Will to get into a cast.
The Federal rail inspector knows cargo characteristics and railroad physics, but he doesn't know what the red lights on the dispatch office monitoring board mean.
It's quite likely he never had to go to a dispatch office or control center before, he probably exclusively did field work.
Justified, most railroad inspectors do not have control tower or rail-hump training, they do exclusive field and on-the-job working directly with the grunts and the ordering offices.
When they put another locomotive on the track in front of the runaway train, trying to brake it from the front, why didn't they have a second guy on the platform at the back of that locomotive just cross onto the front of the runaway train, go in the cab, and stop it? That's exactly where Will ended up climbing aboard at the end of the movie! Why have the guy hanging from a helicopter, when he could just cross from the front engine to the back one?
The front engine kept, for lack of a better term, bouncing off of 777 - if he timed his jump wrong he'd be killed.
Only because they were trying to slow the train down using that second set of engines. If they'd just matched speed with 777 instead of trying to slow it, there wouldn't have been any bouncing and someone could just walk across. Plus, the engines have walkways. The gap between the locomotives would have been less than it is between unpowered rail cars, as train crews do need to pass between locomotives from time to time, so there wouldn't have been any need to make a dangerous leap.
Once 1206 is coupled to the rear of 777, why not try to hook up the air brakes to the train? Especially once the locomotive brakes are burnt out. It wouldn't be easy, but surely less risky than running along the roof of each car.
The whole running thing is impossible at such speeds anyway. He would get blown off the train if he tried it.