Well the only possible train is the SWC, the MRR goes to Kansas City but doesn't run through KS state.
And, if it was going through Kansas today, it can only be 4(7)
Now something here does make sense... she was on time during her entire run and she left TOP over four hours late. So it did stop en route to Topeka. There's any number of reasons for this and it is certainly not out of ordinary.
The ice scraper could probably be found in the emergency locker with other supplies. And IIRC there are other tools for the crew's use throughout the train that could, hypothetically, be used as weapons (or brandished as such.) It is not entirely impossible that several officers would respond to the scene where a Conductor described a passenger who was brandishing what appeared to be a weapon. I doubt highly that a SWAT team would be called, but who knows.
What REALLY doesn't make a lick of sense is the idea that the entire train was abandoned. The only reason they would do this is an evacuation, and its hard to believe that they would forget somebody during an evacuation, though I suppose it is plausible. However if the train was simply delayed because a freight ahead of them got stuck then there'd be no way the train would be evacuated for that reason alone. I mean, policy is to keep people on the train, and Conductors have kept people on stuck trains for a lot longer than 4 hours. (Trains which also would have less in the way of supplies). Such a simple delay would have the Conductors sit there and wait for dispatch to either re-route them or standby for an order to proceed.
On top of that if there was police intervention that would add to the delay. So if it left TOP 4 hours late, then that needs factored in which means there was only a slight delay of the SWC, then the you know what hit the fan and this got piled up on top of this. Not to mention I'd probably have read about an evacuation somewhere... so really, this story makes sense in parts, however those parts are silly. Sounds like a man behaved badly and got thrown off a train.
If anybody has any more details I'd be interested to see the outcome.
EDIT:
Some other things to think about.
If 4(7) was the right train then a delay going into TOP would happen right at the start of breakfast. Scheduled arrival time into TOP is 05:20, which if there was delay means they were getting up and going to the diner to get breakfast. Perhaps there was a light load and everybody was eating or asleep? I've walked the sleeper half of a consist at meal times and it can seem abandoned, doors closed and locked, nobody walking through the halls... can't hear anything. Of course he'd be stopped by the time he reached the Transdorm by some figure of authority, perhaps the Conductor.