This is speculation and nothing more-
I found the CA test results for my '11. The Federal certification does not list results. There may be completely different tune for the CA model.
http://www.fleet.ford.com/resources/ford/general/programs/emissions/2011_a0101599.pdfAssuming it wasn't a direct cheat, and I am not, the one marginal category was HC. The NOX and CO results were far under allowable.
On this engine the ECU cannot control cam timing, or EGR (not equipped). It can control ignition timing, idle speed, fuel injection parameters.
Assuming the unburned HC is the marginal issue here, a logical place to work is cold start. Pull back timing a couple degrees for a few minutes at start and crack up the fast idle a tad. Possibly hold transmission gears a little longer. This to light off the converter faster. It is my observation that my engine is a little slow to light the converter. A solution like this could mean all the rest of the duty cycle is unchanged after a couple minutes of cold operation.
Of course this is grabbing for straws. But I can't believe in general it is off by much.