Who's diesel are you using? (Supermarket or BP/shell)
A few guys myself included have had issues with EGR/Throttle body and running rough, from supermarket diesel as it seems it's high in sulphur and clogs up injectors and moving bits,
Since I found this out back in 09 on my old 57 year 2.3, I've used BP or Shell all the time, no more issues,