I'm not an EGR expert but it seems to me that you should bypass the EGR valve as it serves no performance purpose, except to preserve trees, not when the turbo is already forcing air into the intake. I'm sure aftermarket solutions exist for getting pass the management.
It doesn't even save the trees. It cuts down slightly on exhaust gasses, but increases fuel consumption, which in turn causes an increase in exhaust gasses. Huge bloody clouds of smoke in fact, once it starts playing up.
I know that aftermarket solutions exist (in DIY form) for Merc, but I don't know the Ford system at all.