You won't see the ABS light turn on, but some XL trucks had 2 wheel ABS vs 4 wheel ABS. You may notice a different feel to the brake pedal when you switch to the other PCM if it is a 2 wheel ABS model.
Do you get a CEL for your EGR delete? With the old PCM vs the new?
Bill could tell us what the difference is between the "N4" vs the "D3", I don't have access to that information. Sorry.