Bigjohnny80 - The ski flap in the back seat can sometimes come unlatched, and rattle around unseen behind the arm rest. It's worth checking that every so often. Also fold the seats down, check for anything loose underneath, then put them back properly, with a good solid thunk. The little plastic indicators next to the release pulls on the seat tops should drop down, hiding the red mark. You also need to make sure the rear seatbelt buckles aren't trapped under the seat, where they can cause all manner of noises.
I ran my JTD for five years before trading it in a few months ago for the V6. In all that time, the only major hiccups were a failed rear wheel bearing, replaced under warranty, and a blocked EGR valve that happened just after the 3 year warranty had expired. Try as hard as I might, I could never get more than 9-10k miles out of a set of front tyres - they always went on the inside shoulder, no matter what combination of adjustments I tried. I blame the local roads.
The only other let down on my car was the paint. It was Nero Metallico, which had a reputation for softness and was dropped from the options soon after I got my car. It stained as soon as you looked at it, chipped badly at the front and round the rear wheel arches (again, I mostly blame the local roads, where the favoured road topping is lethally sharp shards of gravel), and a lump of bird lime on the bonnet burned through lacquer and colour layer to the white primer underneath in just 24 hours. No, I've no idea what the local birds eat, either.
Other than that, it was a joy to own and drive, and the only reason I got rid of it was that I wanted a V6. Now I'm missing that 650 miles to a tankful and trying to convince myself the wonderful sound and extra horses were worth it.