I think you guys are mixing/confusing terminology.
When an ECU update is performed (or any codes are cleared), the ECU will reset its emissions monitors. A monitor is something that simply signals that an internal test was performed. Let's use CAT as an example. If the ECU is updated (and/or codes cleared) the CAT monitor will be reset. When you take the car in for SMOG testing, it is going to fail because the CAT monitor is not set. All this means is that the ECU has not yet run its internal catalytic converter efficiency test. Because the test has not been run, the technician cannot say that the CATs are good. For example, let's say you have someone remove your CATs from your car and reset the ECU. You'll be able to drive for a while with no check engine light so you rush over to the smog shop and say, "hey look, no check engine light... my car is good". Not so fast. The technician will see that the monitor for CAT has not yet been set which means that the CAT test has not been performed. IF the monitor is set AND there is no Check Engine light, THEN the technician will know that your CATs are operating as intended.
OK, so your ECU was update/reset. Now you need to drive your car in order that it has the right opportunity/conditions to run the tests. We have an established route which is <20miles and we can 100% of the time get all of the monitors on a 2005-2006 GT to set. I suspect that the NFGT may not be that different. Ford published some guidelines several years ago that I think may be of help and which I have attached below.