The ECU controlls the ratio of air and fuel, according to the data it gets from sensors. When the engine is cold, it puts more fuel, and when it's hot it puts less and so on. If you don't have an ECU, the injectors won't open, and even the fuel pump won't go on.

Problem with the xr3i injection system installation on 1.3 engine is that the engines are different. The ECU thinks that you have the xr3i engine, but you have a smaller one. What happen is, that it puts more fuel to the block than your engine can burn. My best bet for an ECU to this installation would some custom one, Megasquirt for example.