A crucial question is whether Stratford Station will be able to cope.
As I understand it, people buy Olympic tickets for a three hour period
which presumably means that every three hours or so there will be a major
surge in passengers. If that is correct, will the ticket barriers at Stratford
be sufficient to "process" the resulting hordes or will there be massive congestion?

It is not of course only the train companies who need to perform well.
There is also London Underground. This afternoon, just to provide a
little encouragement for the faint hearted, the Central Line was
suspended between Liverpool Street and Leytonstone because of
a burst main at Mile End. If the Central Line stops at the wrong moment
during the Olympics, there will be total chaos.