Worth making it clear that the "official" ECU upgrade does not involve a change in the ECU but simply the installation of a new calibration.
My car has the standard Duratec engine and the Plus 4 SS exhaust was fitted from new at the factory. We had the same emissions problems with the standard ECU so the issue was very simply correct tuning for the SS exhaust which I have always suspected was changed between the prototype and production. When I fitted the throttle bodies and the Omex ECU the issue of MOT emissions and exhaust smell was resolved.
I do get a slight fuel smell until the engine reaches 70°C at which point the sonda lambda feedback loop starts to more accurately control the mixture (and the cat gets up to operating temperature) but even that could be tuned out with a little more work on the cold running part of the calibration but I could not be bothered. This observation applies to my car and may not have any relevance for the car fitted with the Mazda engine.
I have to say that if I had to change my engine I would definitely go for a VVT engine such as the Mazda fitted to the SS or, a step further, the 2.5 litre Ford with VVT.