I have been told that there is a difference between the injector pop-off calibration in the SO injectors and HO injectors. Supposedly, if this adjustment is not right, it will cause a popping noise from the VP44. I have no idea whether or not it would adversely affect anything all I can say is that, when I ordered my DDII's, a few years ago, I was asked whether they were going into a HO or SO. I was asked again recently when I ordered some EDM injectors from JR.
As for as the ECM being programed differently, would'nt that require a different fueling boxes that tap the pump wire, one for SO's and one for HO's? Yes, I understand that the HO VP44 responds differently to aftermarket fueling boxes than the SO's, but the response difference has more to do with the internal component size of the HO VP44 creating a lower maximum output.
This is coming from someone who is also trying to learn so please take it that as that... .