Audi RS4

ok, so i have the engine ready to go in, i'm using the stock wiring harness in the car and i'm using a conversion harness......blah, blah, blah....all the connectors look good and i see where all of them go, except the altenator female end of plug on the harness, it is a different size than the B16's altenator.

so can i push the pins out on the harness and put them in the B16's plug. and if so how in the hell do find out which wire goes in what slot.

one more thing, will the D series injector plugs work on the B16 injectors?

thanks