Leading off with discrediting the agency making the investigation is not a good sign for the veracity of Salazar's account. I guess they're taking their queues from the master negotiator himself.

Investigation issues aside, is he going to be okay? Is he going to live?

3
He is breathing on his own, that seems a good sign.
And presumably when/if he recovers he can tell what happened.

The Reno newspaper had a fair amount of detail about what Amtrak is saying;

"Trugman said those injuries, particularly the burns, could be attributed to a fall from a moving train.

"I think we have an explanation for that, but I don't want to disclose that right now," he said.

Trugman also described the timeline of events that led to Salazar being found, a key question that the Portland State University student's family says they haven't had answered yet:

9:27 a.m.: A Union Pacific Railroad foreman adjacent to the tracks saw the train pass with an open window on one of its coaches, but did not inform Amtrak at that time.
9:30 a.m.: Salazar's train arrives at the Truckee Amtrak station.
About 11:10 a.m.: A Union Pacific work train found Salazar roughly 3-4 feet from the tracks 4 miles east of town.
About 11:30 a.m.: Truckee Police respond to a call of an injured man lying near the tracks, according to a Truckee Police Department press release.
1:20 p.m.: Amtrak Police are notified that a passenger was found critically injured next to the tracks.
1:25 p.m.: Salazar's train arrives in Sacramento.

Truckee Police Department Chief of Police Robert Leftwich described the segment of track Salazar was found along as infrequently traveled.
"There are no pedestrian access points; there's no vehicle access points; it's not easily walked to or driven to," Leftwich said. "You have to be there with purpose."

Trugman also said that the open window was not a passenger window, but a window used by conductors and train employees, although it is accessible to passengers. The window was attached to one of the exit doors.
At that point on the tracks, the train would have been going roughly 40 mph, according to Trugman."<<<<

Another story quoted Trugman saying Amtrak had questioned the friend Salazar met on the train and that there had been no altercation.

If a struggle that caused the horrific injuries Salazar suffered took place on the train surely someone would have heard?
If he was found four miles east of Truckee presumably he fell/jumped/was thrown off before the train reached the station?

A story quoted the Truckee police chief stating that Salazar did not get off the train at the Truckee station but it did not say how he knew that.