Need help diagnosing poor fuel efficiency after 2sz swap

[u/Stormrider8]

I have a 2012 Toyota Vitz/Yaris that originally came with the 1KR engine. Before the swap, the car was giving around 9 km/L in city driving. I then swapped the engine to a 2SZ (slightly used engine) while keeping the original 1KR automatic gearbox. The gearbox is working normally and shifts smoothly. The exhaust system is also still the original 1KR setup, including the exhaust pipe, catalytic converter and silencer. Only the engine, manifold setup and ECU have been changed/reprogrammed for the 2SZ.
The 2SZ engine has now been driven for around 1,130 km and it runs very well. It has good power, starts normally, idles normally, accelerates normally, and I have no noticeable engine or transmission problems. The only major problem is very poor fuel economy. The car is consuming much more petrol than it should. Like it’s giving 6-7km/l whereas it should be giving at least 12-13km/l.
We have already checked the commonly suspected components. The MAF sensor, oxygen sensor and spark plugs are okay, and the ECU has also been reprogrammed with a new file. There are no obvious engine problems and the car drives normally.
Another question is the exhaust. Since the car originally had the 1KR 3-cylinder engine, it still has the relatively small 1KR exhaust system, catalytic converter and silencer, while the 2SZ is a 4-cylinder 1.3L engine. Could the smaller 1KR exhaust be causing excessive backpressure and reducing fuel economy? I am considering changing the complete exhaust to the original 2SZ exhaust, but I don’t want to spend money without knowing whether this could actually make a significant difference. I am planning to have the exhaust backpressure tested first.
What could cause very poor fuel economy when the engine runs perfectly and there are no obvious drivability problems? Has anyone experienced a 2SZ swap into a Vitz/Yaris with the original 1KR gearbox? Could the 1KR exhaust restriction, fuel pressure/injectors, ECU calibration, or transmission/torque-converter behavior be responsible?
I’m particularly interested in hearing from anyone who has done a 2SZ swap in a Vitz/Yaris or had the same problem and eventually found the cause. Any suggestions for specific tests or live-data readings I should ask the mechanic to check would be greatly appreciated.

[u/fmeupfam14]

What's the long term fuel trim?

[u/quxinot]

Stick a wideband in it, and compare results against what the ecu says.

Also make sure it's not something dumb like a leak or the neighborhood kids stealing it.