1) The VSS change was between 1999 an 2000

2) The 01+ CD4E has a .810" chain (and thus smaller pitch sprockets) and the pre 01 CD4E has a 1.05" chain. I would imagine that the shift strategy combined with the smaller (thus lighter) components would make for less rotational losses and thus less driveline loss.
3) Sometime in late 98 IIRC, Ford revised the oil pump.