I think your ideas about the trays and cross-contamination are very interesting. However I'm not quite following you about the postmarking. Are you saying that mail with pre-printed stamps are handled differently, I presume, than other letters would? If one mailed a letter from Florida with a pre-printed stamp to New York or D.C. addresses it would not be post-marked in Florida but in Trenton NJ?
Plus, major mail generation (and mail collection) operations occur BEFORE 7 PM Friday evening. USPS doesn't even process mail on Sunday although it does fly it around the country, or dispatch it on trucks.
People do not mail much stuff on the weekends. It's easy for the handful of pieces entered late on a Friday evening (after last prayers at the mosque) to get lost for a few days ~ in fact, the system is virtually designed to ensure that this happens!
My thesis is that everything happened normally, and that the terrorists could not possibly have anticipated things going down this way.