To be clear, I do not think the plotted times are off. In fact, I think they're quite accurate--missing 22:04 notwithstanding.
The problem is that getting absolute precise location measurements are difficult, for example, when comparing where the jet would be on the Western Flight Path versus the FBI Flight Path.
I quite painstakingly went through all of the radio transcripts that provided air speed, temperature, atmosphere, wind direction and the like to determine as precisely as possible the ground speed--which needless to say is critically important. From what I could tell everything appeared to add up.