You're missing two points Sandman:
1) When Ford builds (and stockpiles) an EEC, it is already flashed with its code. Has to be, so they can be tested (and assigned a part number) before they are put in a box. So, no matter if the 95 Contour was EEC-IV or EEC-V, there still have to be a few boxes somewhere specifically for 95 Contours. Ford doesn't have a single "blank" PCM sitting around a warehouse waiting for a code flash.
2) Developing initial EEC-V applications early (i.e. for 95MY) for an established engine exposes Ford to less design risk than trying to do it on a brand new engine. The sensors, packaging, etc. were much less likely to move around on a 95 Windstar 3.8L OHV engine (already well established) than on a brand new engine in a brand new car. So, the guys designing the EEC-V had a pretty well established (and well understood) engine to work with, instead of an engine that could change for a variety of reasons prior to launch.
This is conjecture, but I would not be surprised if the Duratec design was kicked off internally to Ford before the EEC-V, thus the engine was originally planned with an EEC-IV system. Switching to EEC-V midstream would throw timing way off. Most likely, there was a parallel EEC-V team working on the 96 once it was identified as a need.
Also, the material cost of an EEC-IV is less than an EEC-V (as well as variable cost in 1994 - economies of scale), thus allowing the program to meet its cost/price goals more easily (a VERY important measurable in a new vehicle launch). When they went to EEC-V in 96 either the selling price had to increase, the material content had to decrease, or the per unit profit had to decrease. We all know what Ford prefers to do in this situation. :rolleyes:
Trust me on this; I used to draw a paycheck as an engineer at the plant that makes these parts. I also worked closely with the engineer responsible for developing some of the new processes for the EEC-V. Ford didn't choose the method if EEC-V introduction that would cost them more money when looking at the big picture.
