This conversion has been done before loads of times using the 1.8 ECU and injectors. They are virtually identical engines except for the capacity, only the fuelling needs adjusting.

The MAF sensor is perfectly capable of recognising the increased air flow and telling the ECU to compensate for it, it will then increase the fuel flow. At the moment it's recognising an increased air flow and compensating by increasing the fuel...The trouble is that it's working on the basis of 1.8 injectors when it has 2.0 injectors fitted...It's running rich, trust me on this, I've seen this problem before.

BTW, this might not be the only problem but it is a problem. With all else being well your car will run perfectly on 1.8 injectors.