I was just looking through the MoT handbook and the part on emissions isn't all that easy to read but it does say that if a car is fitted with another engine (of whatver make) then the emissions test carried out is to be the one for the age of the engine, not of the car.
That means I can replace my knackered 2.0 omega engine with my not-so-knackered carlton engine and and not worry too much about emissions!? ...or cats or weird valves.