With modifications that extensive, he will need a custom dyno tune with wideband O2 sensors to get the correct air/fuel ratio.
You can get it to run with the stock ECU, but getting it to run efficiently is a whole other issue. First of all, is he running 30# or 42# injectors? With that combo 30# injectors should be plenty. With 42# injectors, he'll have a hard time getting it do anything but run rich, even if he turns the fuel pressure down with an adjustable fuel pressure regulator (which he should also have). I also assume he has a mass air meter that is calibrated for whichever injector size he has? If not... there's the problem right there.
Also, what exactly do you mean by not running well? Is it missing, dies at idle, just isn't making power???