Bill,
You've got 50% right so far...but still looking for the other half of the question, and I won't say what part of your answer is right.
Yes, they had unending problems at that race with gearboxes, almost to the point where they could set their watches by the time that they failed based upon service life. Every one of the cars had a gearbox change during that weekend of racing, but I'm looking for something that was different with just one of the MKIV entries other than the one that you just stated. Hint: It also has to do with something cosmetic, but it also involved a change from the norm with the Ford teams.