The locomotive pulling the train is a 1500hp EMD GP7, which was built in the 1950s. All of these have been retired for many years from mainline service. Also, this is supposedly a long-haul mixed freight, which would be much longer than the 1000 or so feet it is, with multiple modern 4400hp locomotives, and would be running (from descriptions by Lydia) on the BNSF Railway's Transcon line, a modern double-track mainline, not the obviously forlorn single-track branch line used in this episode.
When the train approaches, Walt, Jesse, and Todd are under the bridge as it passes over; it has not started to brake yet. Shortly after that shot, the train comes around a slight bend and the engineers see the truck and apply the brakes (in reality when shot, the train is actually approaching the bridge again). At this point there wouldn't be enough time/distance for the train to stop before hitting the truck. When measuring the distance earlier, Jesse states "814" as the distance from the road to the bridge. It's likely 814 feet (in reality, it is). Regardless if that's 814 feet or meters, the train couldn't cross the bridge at speed and stop in time.
The shot of the excavator lowering the tanks in the ground is at a different location. In that shot, there's a good amount of grass behind the pile of dirt. In the next shot when the water truck is backing up to the buried tanks (and in other wide shots of the buried tanks) no grass is nearby.
Lydia describes the transport of the methylamine as starting at Long Beach [California?] (it was manufactured in China). She pulls out a map and shows Walt, Jessie & Mike the route of the train about which she declares "...which travels East..."
After the transfer of methylamine and water from the train to the tanks in the ground, they have two choices. Either lift the tank full of methylamine out of the ground, or pump the methylamine out of the ground into another 1,000 gallon tank to haul away. The first option is unlikely - 1,000 gallons weighs approximately 8,300 lbs or about 4.15 tons. So they must have pumped it out into another 1,000 gallon tank. Of course, this is one of those scenes we don't see - we just assume it gets done.
However, the next time we see the methylamine is it is in a tank, horizontally, on a trailer and being hauled by a car. Even setting aside the weight of the trailer, I am not sure there are any cars that can haul 4.15 tons - maybe a large pick-up truck or maybe a large SUV - but a car?
On the same day that they bury the tanks, Walt, Mike, and Jesse measure the distance from the intersection where they plan to create an obstruction to the car carrying methylamine. This would be impossible for them to know until 6 hours before the robbery, when Lydia gave them the train manifest.
Mike, Walt and Jessie had taken Lydia to a warehouse(?) with a view to kill her. She describes a process whereby the guys may rob a train of methylamine. She describes the process by the use of a map. WHERE by G*d's good grace did that victim ever have the facility to pull a map out of her one of her orifice(s) by which she could show the guys how to obtain an "Ocean" of Meth'?