There are versions of the 2.8 JTD with, and without EGR, but eLearn states that versions with EGR, are also fitted with a catalytic converter.
My 2006 2.8 JTD has neither.
Have you confirmed that yours has EGR fitted?
Many years ago I rented a Ford Transit PVC in NZ. The engine developed an alarming rattle, which I eventually linked to coasting (minimum throttle) situations, when the engine was at normal operating temperature. We lost confidence in the vehicle, and had it replaced. I was later told that the case of the problem was a stuck EGR valve.
Another possibility is diesel "knock", which can sound very mechanical, and IIRC is caused by too advanced injection.,