Not sure about the fuel injection. But it should not be the issue. I have herd them click and clat a little but a full on knock is not efi unless its from a badly leaking injector.
I would be willing to bet its a loose rod bolt.
That being said did you clearence the block for the larger crank. Most of the time they fit but sometimes they just bearly touch and will make noise.
I have also seen a flex plate make some aweful noise. But usally that does not go away when a plug is pulled.
How hard is it to get the oil pan off?